JP2006031308A - Apparatus, method, and program for designing nucleic acid array, apparatus, method, and program for calculating function impediment effect, and apparatus, method, and program for calculating degree of function impediment effect - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To design an array of an siRNA impeding the function of a target gene, also taking a non-target gene having a low homology into consideration. <P>SOLUTION: The base sequence of the siRNA is designed using a nucleic array design apparatus 100 including: a candidate array acquisition portion 200 for acquiring the base sequence of siRNA candidates; to the base sequence acquired in the candidate array acquisition portion 200, an activity score calculation portion 300 for calculating an activity score indicating a degree of impeding the function of the gene by the base sequence; an effect score calculation portion 400 for calculating an effect score indicating a degree of impeding the function of the non-target gene by the base sequence acquired by the candidate array acquisition portion 200; and an impeding array decision portion 500 for deciding the base sequence of the siRNA, based on the activity score and the effect score. <P>COPYRIGHT: (C)2006,JPO&NCIPI

Description

  The present invention relates to a nucleic acid sequence design device, a nucleic acid sequence design method, a nucleic acid sequence design program, a function inhibition effect calculation device, a function inhibition effect calculation method, a function in a nucleic acid sequence design that has a specific action on a target gene. The present invention relates to an inhibition effect calculation program, a function inhibition influence degree calculation device, a function inhibition influence degree calculation method, and a function inhibition influence degree calculation program.

A double-stranded nucleic acid having a length of about 21 residues and having an overhang of 2 residues T (thymine) at both ends is called siRNA (Short Interfering RiboNucleic Acid), and is a nematode, fly, mammal, plant In cells of many organisms such as, it is known to inhibit the function by suppressing cleavage of mRNA (messenger RNA) having a complementary sequence and translation into protein.
When this siRNA is introduced into a cell, only one of the two strands in the cytoplasm is incorporated into a complex called RISC (RNA Induced Silencing Complex), and RISC is a sequence complementary to the sequence of the incorporated nucleic acid. This mRNA is cleaved by binding to mRNA having By utilizing this property of siRNA, siRNA for a specific gene is prepared and introduced into a living body, and the gene is suppressed, thereby enabling gene function analysis experiments and gene therapy.

  A nucleic acid that inhibits the function of a gene such as siRNA is referred to as a function-inhibiting nucleic acid.

FIG. 1 is a diagram showing the flow of siRNA sequence design processing in the prior art.
In the conventional siRNA sequence design method shown in FIG. 1, first, an mRNA sequence transcribed from a target gene is input (S1).
All 21-residue sequences are extracted from the input mRNA sequence, and each is used as a siRNA candidate sequence (S2).
The activity is predicted for the siRNA candidate sequence using several indices, and the degree is scored (S3).
In the scoring, if the siRNA sequence completely matches the sequence of the non-target gene, the siRNA sequence is excluded from the candidate sequences.
A siRNA sequence having a high score of activity is determined (S4).

  The conventional siRNA sequence design method follows only the principle of siRNA degradation action of siRNA. It is known that the degradation effect of siRNA mRNA is almost ineffective when there is a mismatch of about one base, and therefore, only a candidate sequence of siRNA that completely matches the sequence of the non-target gene is removed. ing.

  However, by introducing siRNA, it is reported that the expression of a mismatched mRNA whose sequence is about 1 or that of the siRNA or that the translation of a protein from mRNA having a mismatch of 3 to 4 bases is inhibited. Has been.

For example, it has been clarified that introduction of siRNA causes inhibition of translation from mRNA to protein having the same sequence as siRNA, in the same way that microRNAs endogenous to living organisms inhibit translation into proteins. (Non-Patent Document 1).
For example, if the target gene coding region or 3'UTR (UnTranslated Region) sequence contains a sequence that is homologous to the siRNA by allowing a mismatch of 3 to 4 bases, the example shows the effect of sufficient translation inhibition. ing.

Moreover, since siRNA has a chemical structure almost identical to that of microRNA, it is considered that siRNA is incorporated into RISC by the same mechanism as microRNA and causes translational inhibition.
microRNA follows the following production process, and at a certain stage, the chemical structure is similar to siRNA.
The production process of microRNA will be explained. First, it is transcribed from the genome as RNA having a stem loop structure, and then excised as double-stranded RNA having a phosphate group at the 5 'end and an overhang of 2 residues at the 3' end. Later, one of the strands is incorporated into the RISC as microRNA.
microRNA has a chemical structure similar to siRNA at the stage of double-stranded RNA.
It has been reported that microRNA inhibits translation from mRNA to protein if there is a sequence that matches 8 residues at the 5 ′ end of the microRNA in the coding region of mRNA or the sequence of 3′UTR ( Non-patent document 2).
For this reason, even siRNA may inhibit protein translation from mRNA having a sequence homologous to 8 residues on the 5 ′ end side.
Saxena et al., 2003, Small RNAs with impact match to endogenous mRNA repression translation, The journal of biochemical 278: 44312-44319. Lai et al., 2002, MicroRNAs are complementary to 3′UTR motifs mediate negative post-transcriptional regulation, Nature genetics, 30: 363-364.

Thus, when designing siRNA, if the effect on a gene (hereinafter referred to as a non-target gene) other than the target gene (hereinafter referred to as a target gene) is not taken into consideration, the intended use purpose of siRNA Produces undesirable results.
That is, in the siRNA sequence design method according to the prior art, since low homology is not expected, the expression of a non-target gene is unexpectedly suppressed in a cell into which the designed siRNA is introduced.

  Therefore, an object of the present invention is to design an siRNA sequence that inhibits the function of a target gene and also takes into consideration a non-target gene having low homology.

  The nucleic acid sequence design apparatus of the present invention inputs a data on a gene of a target organism, acquires a candidate sequence acquisition unit that acquires a candidate of a base sequence of a function-inhibiting nucleic acid based on the input data on the gene, and acquires a candidate sequence The activity score calculation unit that calculates the activity score indicating the degree to which the base sequence inhibits the function of the gene with respect to the acquired base sequence, and the base sequence acquired by the candidate sequence acquisition unit The base obtained by the candidate sequence obtaining unit based on the influence score calculating unit that calculates the influence score indicating the degree of influence to be inhibited, the activity score calculated by the activity score calculating unit, and the influence score calculated by the influence score calculating unit And an inhibitory sequence determination unit that determines a base sequence from sequence candidates and outputs the determined base sequence as a designed base sequence.

  The nucleic acid sequence design apparatus of the present invention inputs a data on a gene of a target organism, acquires a candidate sequence acquisition unit that acquires a candidate of a base sequence of a function-inhibiting nucleic acid based on the input data on the gene, and acquires a candidate sequence Activity score for calculating the activity score indicating the degree to which the base sequence inhibits the function of the gene based on the type of residue constituting the base sequence and the position in the base sequence Based on the activity score calculated by the calculation unit and the activity score calculation unit, the base sequence is determined from the base sequence candidates acquired by the candidate sequence acquisition unit, and the determined base sequence is output as the designed base sequence And a section.

  The nucleic acid sequence design apparatus further targets the function-inhibiting nucleic acid when each residue is present at each position of the base sequence with respect to the type of residue constituting the base sequence and the position in the base sequence. An inhibition correlation value storage unit that stores a degree of inhibition of the function of the gene as an inhibition correlation value, and the activity score calculation unit is configured to acquire the candidate sequence acquisition unit based on the inhibition correlation value stored in the inhibition correlation value storage unit The activity score of the obtained base sequence is calculated.

The inhibition correlation value stored in the inhibition correlation value storage unit is data based on a known nucleic acid indicating a function-inhibited nucleic acid whose presence or absence of inhibition of the function for the target gene is known, and F (m, n) is a position m Shows the inhibition correlation value when residue n is present in Q, and Q (m, n) is the ratio of the known nucleic acid that inhibits function to the presence of residue n at position m among the known nucleic acids that inhibit function P (m, n) represents the proportion of residue n at position m relative to all known nucleic acids,
F (m, n) = log {Q (m, n) / P (m, n)}
It is characterized in that it is required.

  The activity score calculation unit includes at least one of guanine and cytosine in the base sequence, the presence / absence of four or more consecutive portions, the GC content indicating the content of guanine and cytosine in the base sequence, and the target gene The activity score of the base sequence acquired by the candidate sequence acquisition unit is calculated based on at least one of the position of the base sequence and the homology between the non-target gene and the base sequence.

  The nucleic acid sequence design apparatus of the present invention inputs a data on a gene of a target organism, acquires a candidate sequence acquisition unit that acquires a candidate of a base sequence of a function-inhibiting nucleic acid based on the input data on the gene, and acquires a candidate sequence The candidate sequence acquisition unit acquires the influence score calculation unit that calculates the influence score indicating the degree of influence that inhibits the function of the non-target gene, and the influence score calculated by the influence score calculation unit. And an inhibitory sequence determination unit for determining a base sequence from the determined base sequence candidates and outputting the determined base sequence as a designed base sequence.

  The nucleic acid sequence design apparatus further provides a function-inhibiting nucleic acid when a residue is present at each position of the base sequence with respect to the type of the residue constituting the base sequence and the position in the base sequence. An inhibition correlation value storage unit that stores the degree of inhibition of the function of the target gene as an inhibition correlation value, and the influence score calculation unit obtains the candidate sequence based on the inhibition correlation value stored in the inhibition correlation value storage unit The influence score of the base sequence acquired by the part is calculated.

The inhibition correlation value stored in the inhibition correlation value storage unit is data based on a known nucleic acid indicating a function-inhibited nucleic acid whose presence or absence of inhibition of the function for a non-target gene is known, and F (m, n) is a position Inhibition correlation value when residue n is present in m, Q (m, n) is a known nucleic acid that inhibits function, and residue n is present at position m among known nucleic acids that inhibit function P (m, n) represents the proportion of residue n at position m relative to all known nucleic acids,
F (m, n) = log {Q (m, n) / P (m, n)}
It is characterized in that it is required.

  The influence score calculation unit, when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid, at least one of the amount of genetic information expressed from the non-target gene and the functional importance of the non-target gene, The influence score of the base sequence acquired by the candidate sequence acquisition unit is calculated based on the inhibition correlation value stored in the inhibition correlation value storage unit.

  Based on the inhibition correlation value stored in the inhibition correlation value storage unit and the homology between the base sequence of the non-target gene and the base sequence of the function-inhibiting nucleic acid, the influence score calculation unit The influence score of the acquired base sequence is calculated.

  The influence score calculation unit, when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid, at least one of the amount of genetic information expressed from the non-target gene and the functional importance of the non-target gene, Based on the inhibition correlation value stored in the inhibition correlation value storage unit and the homology between the base sequence of the non-target gene and the base sequence of the function-inhibiting nucleic acid, the influence score of the base sequence acquired by the candidate sequence acquisition unit is calculated. It is characterized by calculating.

  The said influence score calculation part calculates the influence score of the base sequence which the said candidate sequence acquisition part acquired based on the homology of the base sequence of a non-target gene, and the base sequence of a function inhibition nucleic acid, It is characterized by the above-mentioned.

  When the non-target gene is not inhibited by the function-inhibiting nucleic acid, the influence score calculation unit calculates at least one of the amount of genetic information expressed from the non-target gene and the functional importance of the non-target gene, Based on the homology between the target gene and the base sequence, the influence score of the base sequence acquired by the candidate sequence acquisition unit is calculated.

  The candidate sequence acquisition unit acquires a genetic information sequence indicating a base sequence of genetic information as data related to a gene of a target organism from a storage unit that stores a base sequence related to a gene of a biological species to which the target organism belongs. A type sequence acquisition unit is provided, and the candidate sequence acquisition unit acquires a base sequence candidate of a function-inhibiting nucleic acid based on the genetic information sequence acquired by the type sequence acquisition unit.

  The candidate sequence acquisition unit further inputs a target gene as data relating to the gene of the target organism, and the portion that differs between the base sequence acquired by the type sequence acquisition unit and the base sequence of the target gene of the target organism A different sequence acquisition unit for acquiring the base sequence, a base sequence generation unit for generating a base sequence based on the base sequence acquired by the type sequence acquisition unit and the base sequence acquired by the different sequence acquisition unit, The candidate sequence acquisition unit acquires a candidate for a base sequence of a function-inhibiting nucleic acid based on the base sequence generated by the base sequence generation unit.

  The candidate sequence acquisition unit is configured to input a target gene as data relating to a gene of a target organism, acquire a base sequence from the target gene of the target organism, and a biological species to which the target organism belongs The target organism from the storage unit that stores the base sequence of each gene separately into a genetic information region sequence indicating the base sequence of the genetic information region and a non-genetic information region sequence indicating the base sequence of the non-genetic information region As the data related to the gene, the type region sequence acquisition unit for acquiring the genetic information region sequence and the non-genetic information region sequence for the target gene, the base sequence acquired by the base sequence acquisition unit, and the type region sequence acquisition unit Based on the homology between the genetic information region sequence and the non-genetic information region sequence, the genetic information region sequence was extracted from the base sequence acquired by the base sequence acquisition unit and extracted. An information sequence acquisition unit that acquires a genetic information sequence indicating a base sequence of genetic information based on the transmission information region sequence, the candidate sequence acquisition unit based on the genetic information sequence acquired by the information sequence acquisition unit, A candidate for a base sequence of a function-inhibiting nucleic acid is obtained.

  The candidate sequence acquisition unit acquires a candidate of a base sequence of a function-inhibiting nucleic acid from a storage unit that stores a base sequence candidate of the function-inhibiting nucleic acid.

  The nucleic acid sequence design method of the present invention includes a candidate sequence acquisition step of inputting data related to a gene of a target organism, acquiring a candidate of a base sequence of a function-inhibiting nucleic acid based on the input data related to the gene, and acquiring a candidate sequence The activity score calculation step for calculating the activity score indicating the degree to which the base sequence inhibits the function of the gene with respect to the base sequence acquired in the step, and the base sequence acquired in the candidate sequence acquisition step The base obtained in the candidate sequence acquisition step based on the influence score calculation step for calculating the influence score indicating the degree of influence to be inhibited, the activity score calculated in the activity score calculation step, and the influence score calculated in the influence score calculation step Performing an inhibitory sequence determination step of determining a base sequence from sequence candidates and outputting the determined base sequence as a designed base sequence That.

  In a nucleic acid sequence design method for designing a base sequence of a function-inhibiting nucleic acid that inhibits the function of a target gene of a target organism, data on the gene of the target organism is input, and function inhibition is performed based on the input data on the gene. A candidate sequence acquisition step for acquiring nucleic acid base sequence candidates, and a base sequence acquired in the candidate sequence acquisition step based on the types of residues constituting the base sequence and the position in the base sequence An activity score calculation step for calculating an activity score indicating the degree to which the sequence inhibits the function of the gene, and based on the activity score calculated in the activity score calculation step, the nucleotide sequence is obtained from the nucleotide sequence candidates acquired by the candidate sequence acquisition step. An inhibitory sequence determination step of determining and outputting the determined base sequence as a designed base sequence.

  In a nucleic acid sequence design method for designing a base sequence of a function-inhibiting nucleic acid that inhibits the function of a target gene of a target organism, data on the gene of the target organism is input, and function inhibition is performed based on the input data on the gene. A candidate sequence acquisition step for acquiring nucleic acid base sequence candidates, an influence score calculation step for calculating an influence score indicating the degree of influence that the base sequence acquired in the candidate sequence acquisition step inhibits the function of the non-target gene, and an influence Based on the influence score calculated in the score calculation step, the base sequence is determined from the candidate of the base sequence acquired in the candidate sequence acquisition step, and the inhibition sequence determination step of outputting the determined base sequence as the designed base sequence is executed It is characterized by that.

  The nucleic acid sequence design program of the present invention causes a computer to execute the nucleic acid sequence design method.

  The function-inhibiting effect calculation apparatus of the present invention provides each residue at each position of the base sequence with respect to the types of residues constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid. In this case, the inhibition correlation value storage unit for storing the degree of inhibition of the function of the gene by the function-inhibiting nucleic acid as an inhibition correlation value, the base sequence of the function-inhibiting nucleic acid, and the input base sequence of the function-inhibiting nucleic acid and the inhibition And an activity score calculating unit that calculates an activity score indicating the degree to which the input function-inhibiting nucleic acid inhibits the function of the gene based on the inhibition correlation value stored in the correlation value storage unit.

  In the method for calculating the function-inhibiting effect of the present invention, each residue is present at each position of the base sequence with respect to the type of the residue constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid. In this case, the inhibition correlation value storage step for storing the degree of inhibition of the function of the gene by the function-inhibiting nucleic acid as an inhibition correlation value, the base sequence of the function-inhibiting nucleic acid, and the input base sequence of the function-inhibiting nucleic acid and the inhibition And an activity score calculating step of calculating an activity score indicating the degree to which the input function-inhibiting nucleic acid inhibits the function of the gene based on the inhibition correlation value stored in the correlation value storing step.

  The function inhibition effect calculation program of the present invention causes a computer to execute the function inhibition effect calculation method.

  The function inhibition influence calculation apparatus of the present invention provides each residue at each position of the base sequence with respect to the type of the residue constituting the base sequence of the function-inhibited nucleic acid and the position in the base sequence of the function-inhibited nucleic acid. When present, an inhibition correlation value storage unit that stores the degree of inhibition of the function of the non-target gene by the function-inhibiting nucleic acid as an inhibition correlation value and the base sequence of the function-inhibiting nucleic acid are input. When the function is not inhibited, based on the amount of genetic information expressed from the non-target gene, the functional importance of the non-target gene, and the inhibition correlation value stored in the inhibition correlation value storage unit And an influence score calculation unit for calculating an influence score indicating the degree of inhibition of the function of the non-target gene by the base sequence of the input function-inhibiting nucleic acid.

  The function inhibition influence calculation device of the present invention inputs the base sequence of a function-inhibiting nucleic acid, and when the non-target gene is not inhibited by the function-inhibiting nucleic acid, the amount of genetic information expressed from the non-target gene and the non-target Based on at least one of the functional importance of the gene and the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, the degree to which the input function-inhibiting nucleic acid inhibits the function of the non-target gene is determined. An influence score calculation unit for calculating an influence score is provided.

  The function inhibition influence calculation apparatus of the present invention provides each residue at each position of the base sequence with respect to the type of the residue constituting the base sequence of the function-inhibited nucleic acid and the position in the base sequence of the function-inhibited nucleic acid. If present, the inhibition correlation value storage unit that stores the degree of inhibition of the function of the non-target gene by the function inhibiting nucleic acid as an inhibition correlation value, and the base sequence of the function inhibiting nucleic acid are input and stored in the inhibition correlation value storage unit. Based on the inhibition correlation value and the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, an influence score indicating the degree to which the base sequence of the input function-inhibiting nucleic acid inhibits the function of the non-target gene is calculated. And an influence score calculation unit for calculating.

  The function inhibition influence calculation apparatus of the present invention provides each residue at each position of the base sequence with respect to the type of the residue constituting the base sequence of the function-inhibited nucleic acid and the position in the base sequence of the function-inhibited nucleic acid. When present, an inhibition correlation value storage unit that stores the degree of inhibition of the function of the non-target gene by the function-inhibiting nucleic acid as an inhibition correlation value and the base sequence of the function-inhibiting nucleic acid are input. When the function is not inhibited, at least one of the amount of genetic information expressed from the non-target gene and the functional importance of the non-target gene, the inhibition correlation value stored in the inhibition correlation value storage unit, and the non-target An influence score calculation unit for calculating an influence score indicating the degree of inhibition of the function of the non-target gene based on the homology between the gene and the base sequence of the input function-inhibiting nucleic acid. And it said that there were pictures.

  In the method for calculating the degree of influence of function inhibition of the present invention, each residue is located at each position of the base sequence with respect to the type of the residue constituting the base sequence of the function-inhibited nucleic acid and the position in the base sequence of the function-inhibited nucleic acid. When present, an inhibition correlation value storing step for storing the degree of inhibition of the function of the non-target gene by the function-inhibiting nucleic acid as an inhibition correlation value, and the base sequence of the function-inhibiting nucleic acid are input. When the function is not inhibited, based on the amount of genetic information expressed from the non-target gene, the functional importance of the non-target gene, and the inhibition correlation value stored in the inhibition correlation value storage step And an influence score calculation step of calculating an influence score indicating the degree to which the base sequence of the input function-inhibiting nucleic acid inhibits the function of the non-target gene.

  The method for calculating the degree of influence of function inhibition according to the present invention is the method of inputting the base sequence of a function-inhibiting nucleic acid, and the amount of genetic information expressed from the non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid. Based on at least one of the functional importance of the gene and the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, the degree to which the input function-inhibiting nucleic acid inhibits the function of the non-target gene is determined. An influence score calculation step of calculating an influence score to be shown is executed.

  In the method for calculating the degree of influence of function inhibition of the present invention, each residue is located at each position of the base sequence with respect to the type of the residue constituting the base sequence of the function-inhibited nucleic acid and the position in the base sequence of the function-inhibited nucleic acid. If present, the inhibition correlation value storing step for storing the degree of inhibition of the function of the non-target gene by the function inhibiting nucleic acid as an inhibition correlation value and the base sequence of the function inhibiting nucleic acid are input and stored in the inhibition correlation value storing step. Based on the inhibition correlation value and the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, an influence score indicating the degree to which the base sequence of the input function-inhibiting nucleic acid inhibits the function of the non-target gene is calculated. An influence score calculation step is calculated.

  In the method for calculating the degree of influence of function inhibition of the present invention, each residue is located at each position of the base sequence with respect to the type of the residue constituting the base sequence of the function-inhibited nucleic acid and the position in the base sequence of the function-inhibited nucleic acid. When present, an inhibition correlation value storing step for storing the degree of inhibition of the function of the non-target gene by the function-inhibiting nucleic acid as an inhibition correlation value, and the base sequence of the function-inhibiting nucleic acid are input. When the function is not inhibited, at least one of the amount of genetic information expressed from the non-target gene and the functional importance of the non-target gene, the inhibition correlation value stored in the inhibition correlation value storing step, and the non-target Based on the homology between the gene and the base sequence of the entered function-inhibiting nucleic acid, the impact score calculator calculates the impact score that indicates the degree to which the base sequence of the input function-inhibited nucleic acid inhibits the function of the non-target gene. And executes and.

  The function inhibition influence degree calculation program of the present invention causes a computer to execute a function inhibition influence degree calculation method.

  The candidate sequence acquisition unit stores a genetic information sequence indicating a genetic information base sequence as a target gene from a storage unit that stores a base sequence related to a gene of a species to which the target organism belongs. And a non-target gene to obtain a type sequence acquisition unit, and the candidate sequence acquisition unit acquires a candidate of a base sequence of a function-inhibiting nucleic acid based on the genetic information sequence of the target gene acquired by the type sequence acquisition unit. The influence score calculation unit calculates the influence score based on the homology between the genetic information sequence of the non-target gene acquired by the type sequence acquisition unit and the base sequence of the function-inhibiting nucleic acid acquired by the candidate sequence acquisition unit. It is characterized by that.

  The candidate sequence acquisition unit further inputs a target gene and a non-target gene as data relating to the gene of the target organism, the base sequence of the target gene acquired by the type sequence acquisition unit, and the target of the target organism Obtain the base sequence of the portion that differs from the base sequence of the gene, the base sequence of the non-target gene acquired by the above-mentioned type sequence acquisition unit, and the base sequence of the portion that is different from the base sequence of the non-target gene of the target organism. Base sequence of the target gene of the target organism based on the base sequence of the target gene acquired by the different sequence acquisition unit and the base sequence of the target gene acquired by the different sequence acquisition unit A target sequence based on the base sequence of the non-target gene acquired by the type sequence acquisition unit and the base sequence of the different part of the non-target gene acquired by the different sequence acquisition unit. A base sequence generation unit that generates a base sequence of the non-target gene, and the candidate sequence acquisition unit generates a base sequence candidate of the function-inhibiting nucleic acid based on the base sequence of the target gene generated by the base sequence generation unit. The influence score calculation unit calculates the influence score based on the homology between the base sequence of the non-target gene generated by the base sequence generation unit and the base sequence of the function-inhibiting nucleic acid acquired by the candidate sequence acquisition unit. It is characterized by doing.

  The candidate sequence acquisition unit inputs a target gene and a non-target gene as data relating to the gene of the target organism, acquires the base sequence of the target gene from the target gene of the target organism, A base sequence acquisition unit for acquiring a base sequence of a non-target gene from a target gene, a base sequence of each gene possessed by a species to which the target organism belongs, a genetic information region sequence indicating a base sequence of the genetic information region, Acquires the genetic information region sequence and non-genetic information region sequence for the target gene as data related to the gene of the target organism from the memory unit that stores the genetic information region base sequence indicating the base sequence of the genetic information region. The type region sequence acquisition unit for acquiring the genetic information region sequence and the non-genetic information region sequence for the non-target gene, the base sequence acquired by the base sequence acquisition unit, and the species Based on the homology between the genetic information region sequence obtained by the region sequence obtaining unit and the non-genetic information region sequence, the genetic information region sequence is extracted from the base sequence obtained by the base sequence obtaining unit, and the extracted genetic information region sequence An information sequence acquisition unit that acquires a genetic information sequence indicating a base sequence of genetic information for a target gene and a non-target gene, and the candidate sequence acquisition unit includes the target gene acquired by the information sequence acquisition unit. Based on the genetic information sequence, a candidate for the base sequence of the function-inhibiting nucleic acid is obtained, and the influence score calculation unit acquires the genetic information sequence of the non-target gene acquired by the information sequence acquisition unit and the candidate sequence acquisition unit An influence score is calculated based on the homology with the base sequence of the function-inhibiting nucleic acid.

  According to the present invention, it is possible to calculate an influence score indicating the degree of influence that inhibits the function of a non-target gene.

  Thereby, based on the calculated influence score, it is possible to design a sequence of siRNA taking into consideration a non-target gene having low homology.

  Further, according to the present invention, an activity score indicating the degree of influence that inhibits the function of a target gene can be calculated.

  Thereby, based on the calculated activity score, it is possible to design an siRNA sequence that is effective in inhibiting the function of the target gene.

  By combining these, based on the calculated activity score and influence score, it is possible to design a siRNA sequence that is effective in inhibiting the function of the target gene and also takes into account non-target genes with low homology. it can.

  In other words, since it includes means for strictly predicting the action on non-target genes based on the genetic information of the organism that is the target of siRNA action, it exerts a high effect only on the target gene, and other non-target genes SiRNA sequences that do not affect the sequence can be obtained.

Embodiment 1 FIG.
FIG. 2 is a configuration diagram of the nucleic acid sequence designing apparatus 100 according to the first embodiment.
The configuration of the nucleic acid sequence design apparatus 100 according to Embodiment 1 will be described with reference to FIG.

  The nucleic acid sequence designing apparatus 100 includes the following.

A type information sequence storage unit 181 that stores the base sequence of the mRNA of the gene of the species to which the target organism belongs, the function of which is inhibited by the siRNA to be designed.
A type sequence acquisition unit 210 that acquires the base sequences of the target gene and non-target gene mRNA of the target species from the type information sequence storage unit 181.
A candidate sequence acquisition unit 200 that acquires an mRNA base sequence and siRNA base sequence candidates (hereinafter referred to as siRNA candidate sequences) based on the mRNA base sequence acquired by the type sequence acquisition unit 210.

The degree of inhibition of the function of the target gene when each residue is present in each position of the base sequence, relative to the type of residue constituting the base sequence of siRNA and the position in the base sequence of each base. An inhibition correlation value storage unit 191 that stores the inhibition correlation value.
A gene information storage unit 192 that stores values of gene expression level and functional importance as weighted information values.

  The base sequence of the target gene mRNA and the siRNA candidate sequence are input from the candidate sequence acquisition unit 200, the inhibition correlation value for the input siRNA candidate sequence is acquired from the inhibition correlation value storage unit 191, and the acquired inhibition correlation value is input. An activity score calculation unit 300 that calculates an activity score based on mRNA.

  The base sequence of the mRNA of the non-target gene and the siRNA candidate sequence are input from the candidate sequence acquisition unit 200, and the inhibition correlation value for the input siRNA candidate sequence is acquired from the inhibition correlation value storage unit 191, and also corresponds to the input mRNA. An influence score calculation unit 400 that obtains a weighting information value of a gene to be obtained from the gene information storage unit 192 and calculates an influence score based on the acquired inhibition correlation value and the weighting information value.

  The siRNA candidate sequence acquired by the candidate sequence acquisition unit 200, the activity score calculated by the activity score calculation unit 300, and the influence score calculated by the influence score calculation unit 400 are input, and based on the input activity score and influence score An inhibitory sequence determination unit 500 that determines the base sequence of siRNA from the input siRNA candidate sequence.

FIG. 3 is a diagram showing a processing flow of the nucleic acid sequence designing apparatus 100 according to the first embodiment.
The flow of the process of the siRNA sequence design method performed by the nucleic acid sequence design apparatus 100 according to the first embodiment will be described with reference to FIG.

  The nucleic acid sequence design apparatus 100 performs sequence design of inhibitory nucleic acids as follows.

The base sequence of the mRNA of the target gene is obtained (S101).
Moreover, the base sequence of mRNA of a non-target gene is acquired (S102).
Acquisition of the mRNA base sequence of each gene is performed by the type sequence acquisition unit 210 acquiring the mRNA base sequence of the gene of the target biological species from the type information sequence storage unit 181.

Next, siRNA candidate sequences are extracted from the base sequence of the mRNA of the target gene obtained in S101 (S103).
The extraction of siRNA candidate sequences is performed by the candidate sequence acquisition unit 200 extracting all sequences having a length of 19 bp (base pair) from the base sequence of the target gene mRNA as siRNA candidate sequences.

Next, an activity score for the base sequence of the mRNA of the target gene obtained in S101 is calculated for the siRNA candidate sequences extracted in S103 (S104).
A method for calculating the activity score will be described with reference to FIGS.

FIG. 4 is a diagram showing the contents stored in the inhibition correlation value storage unit 191 in the first embodiment.
In FIG. 4, the types of residues include A (adenine), U (uracil), G (guanine), and C (cytosine), and the inhibition correlation value storage unit 191 stores each gene such as gene A and gene B. On the other hand, the inhibition correlation value when each of A, U, G, and C is located at positions 1 to 19 in the siRNA candidate sequence is stored.

The inhibition correlation value stored in the inhibition correlation value storage unit 191 is a value indicating the degree of inhibition of the function for each gene of the base sequence of any siRNA that has already been obtained through experiments or the like.
This inhibition correlation value indicates a larger value as the possibility of the activity of the gene is higher, and indicates a smaller value as the possibility of the absence of the activity is higher.
Here, activity means that siRNA inhibits the function of a gene.
That is, the inhibition correlation value is so large that siRNA inhibits the function of the gene.
F (m, n), which is an inhibition correlation value when residue n is located at position m, is obtained by the following equation.
F (m, n) = log {Q (m, n) / P (m, n)}
Here, P (m, n) and Q (m, n) are expressed by the following equations.
P (m, n) = (number of siRNAs in which the m-th residue is n among all siRNAs) / (number of all siRNAs)
Q (m, n) = (the number of siRNAs in which the m-th residue is n among active siRNAs) / (the number of active siRNAs)

For example, suppose that 27 siRNAs were active as a result of experimentation with 108 siRNAs.
If there are 28 of all siRNAs, that is, 108 siRNAs whose first residue is A, P (1, A) = 28 / 108≈0.26.
Also, assuming that there are 6 active siRNAs, that is, 27 siRNAs whose first residue is A, Q (1, A) = 6 / 27≈0.22.
F (1, A) = log {Q (1, A) / P (1, A)} = log (0.22 / 0.26) = − 0. 07.

The presence or absence of activity can be determined by experiment as follows.
For example, a reporter gene assay is performed using a luciferase gene that causes a luminescence phenomenon by acting as an enzyme in a cell as a reporter gene.
First, a luciferase gene is bound downstream of the promoter of the gene to be tested, and this is bound to a vector such as a plasmid.
Next, the combined vector is introduced into cultured cells such as Escherichia coli, and the cells are cultured.
The relative luminescence amount of luciferase when siRNA is introduced into this cultured cell and when it is not introduced is determined, and the obtained relative luminescence amount is less than a certain value, that is, the inhibition of function by siRNA is more than a certain value. In some cases active.
This amount of luminescence can be measured using an instrument.
The calculation formula is as follows.
siRNA activity = 100 (%)-relative luminescence amount of luciferase (%)
Relative luminescence amount of luciferase (%) = luminescence amount when siRNA is applied / luminescence amount when siRNA is not acted In other words, the more luminescence of luciferase is suppressed, the higher the activity of siRNA.

  Here, the reporter gene is not limited to the luciferase gene, and the method for determining the presence or absence of activity is not limited to the method using the reporter gene assay.

In calculating the activity score using the inhibition correlation value, the activity score calculation unit 300 calculates the activity score using the inhibition correlation value obtained by the above method and stored in the inhibition correlation value storage unit 191.
The value of F (m, n) is acquired for each position of the siRNA candidate sequence, and the total value of the acquired values is used as the activity score.

  For example, when the siRNA candidate sequence is AGCU... AGCU and the gene whose function is inhibited by siRNA in FIG. 4 is gene A, F (1, A) + F (2, G) + F (3, C) The calculation result of + F (4, U) +... + F (16, A) + F (17, G) + F (18, C) + F (19, U) becomes the activity score.

  The greater the value of the activity score, the higher the possibility of function inhibition by siRNA.

FIG. 5 is a diagram showing a flow of activity score calculation processing based on the index in the first embodiment.
The activity score calculation unit 300 calculates an activity score based on the index by the process shown in FIG.

As one of the indexes, it is determined whether the siRNA candidate sequence has four or more consecutive G or C (S201).
As a result of the determination, in the case of an siRNA candidate sequence in which four or more G or C are continuous, this is excluded from the candidate sequence (S202).

Next, as one of the indices, a GC score for the content of G and C of the siRNA candidate sequence (hereinafter referred to as GC content) is obtained (S203).
For example, the GC score is increased when the GC content is 30% to 50%.

Next, as one of the indices, a position score is obtained for the position of the base sequence of the mRNA of the target gene to which the siRNA candidate sequence corresponds (S204).
For example, the position score is increased when the position of the base sequence of mRNA corresponding to the siRNA candidate sequence is 50 bases or more downstream from the start codon.
In addition, the position score is lowered when the position of the base sequence of mRNA corresponding to the siRNA candidate sequence is the untranslated region (UTR) at the 5 ′ end and the 3 ′ end.

Next, as one of the indexes, a homology score is obtained for the homology between the siRNA candidate sequence and the base sequence of the mRNA of the non-target gene (S205).
For example, the homology score is lowered as the number of matching bases increases in the part where the base sequences match each other most.

  The GC score, position score, and homology score obtained based on each index are summed, and the sum is used as the activity score (S206).

  In the activity score calculation process based on the index, another index may be added to the index, or may be calculated based on a part of the index.

  As described above, the activity score calculation unit 300 calculates the activity score based on the inhibition correlation value and the index, but the activity score may be a total value of the activity score based on the inhibition correlation value and the activity score based on the index. The value of either activity score may be used, or the activity score obtained by other processing may be added.

In FIG. 3, next, for the siRNA candidate sequence extracted in S103, an influence score on the mRNA of the non-target gene obtained in S102 is calculated (S105).
A method for calculating the influence score will be described with reference to FIG.

FIG. 6 is a diagram showing a flow of influence score calculation processing in the first embodiment.
The influence score calculation unit 400 calculates an influence score by the process shown in FIG.

  First, the influence score is set to 0 (S301).

  Next, one base sequence of mRNA of the non-target gene is taken out from the base sequence of mRNA input from the candidate sequence acquisition unit 200 (S302).

Next, a homology score is obtained for the homology between the siRNA candidate sequence and the base sequence of the mRNA of the non-target gene extracted in S302 (S303).
For example, the homology score is increased as the number of matching bases increases in the portion where the base sequences match most.

Next, an activity score indicating the degree to which the siRNA candidate sequence inhibits the function is calculated for the non-target gene corresponding to the base sequence of the mRNA extracted in S302 (S304).
The activity score calculation method is the same as the activity score calculation method described with reference to FIG.

Next, the weighting information value of the non-target gene corresponding to the base sequence of mRNA extracted in S302 is acquired (S305).
The weighting information value is stored in the gene information storage unit 192.
The weighting information value includes a value for the expression level of mRNA from the gene and a value for the functional importance of the gene.

As for the expression level of mRNA from a gene, when the expression level of mRNA is small, it can be assumed that the function of the mRNA is not functioning originally, so that the weighting information value is low.
The expression level of this mRNA is determined by fluorescently labeling mRNA extracted from the target organism and species, and then labeling the fluorescently labeled mRNA on a microarray on which a gene having a base sequence complementary to the mRNA base sequence is spotted. It can be measured by a method of hybridizing with a gene and observing the amount of fluorescence after washing.

In terms of functional importance, even if the function of the target gene is inhibited, if the function is not inhibited and the state of the cell is almost unchanged, the value of the weighting information will be low, and depending on the degree of change Thus, the weighting information value is determined.
The value of the weighting information for the degree of change can be set based on the result of a function inhibition experiment using an arbitrary siRNA or knockout individual.

  The weighting information value may be a total value of the value for the expression level and the value for the importance level, or may be one of these values, or other weighting information values may be added.

Next, based on the value for the functional importance acquired in S305, it is determined whether the non-target gene corresponding to the base sequence of the mRNA extracted in S302 is an essential gene (S306).
Special treatment of the fatal effects such as necrosis of cells by inhibiting the function of non-target genes.

  When it is determined that the non-target gene is an essential gene, it is determined whether the activity score calculated in S304 is a value exceeding an arbitrary threshold A (S307).

  If the non-target gene is an essential gene and the activity score exceeds the arbitrary threshold A, the target siRNA candidate sequence is excluded from the candidate sequences (S308).

  Next, the total value of the homology score calculated in S303 and the activity score calculated in S304 is multiplied by the weighted information value acquired in S305, and the multiplied value is added to the value of the influence score (S309).

Next, it is determined whether there is a base sequence of mRNA of a non-target gene for which an influence score is not obtained in the base sequence of mRNA input from the candidate sequence acquisition unit 200 (S310).
When there is a base sequence of mRNA of a non-target gene for which an influence score is not obtained, S202 to S209 are repeated, and an influence score for all non-target genes is calculated.

  The influence score may be calculated based on the homology score, the activity score, and the weighting information value, or may be calculated based on any value or any combination of values. Other influence scores may be added.

In FIG. 3, next, based on the activity score calculated in S104 and the influence score calculated in S105, the base sequence of siRNA is determined from the siRNA candidate sequence acquired in S103 (S106).
A method for determining the base sequence of siRNA will be described with reference to FIG.

FIG. 7 is a diagram showing a flow of siRNA base sequence determination processing in the first embodiment.
The inhibitory sequence determination unit 500 determines the base sequence of siRNA by the process shown in FIG.

  First, siRNA candidate sequences are excluded from those whose activity score for the target gene is smaller than an arbitrary threshold B (S401).

  Next, siRNA candidate sequences are excluded from those whose influence score for non-target genes is greater than an arbitrary threshold C (S402).

  Next, an overall evaluation score is calculated by subtracting the influence score for the non-target gene from the activity score for the target gene for the remaining siRNA candidate sequences (S403).

  Then, the designed siRNA base sequence having a high overall evaluation score is determined (S404).

  Thereby, about each siRNA candidate sequence, what has a high activity score with respect to a target gene, and a low influence score with respect to a non-target gene is employable as a base sequence of siRNA.

  In FIG. 3, the nucleic acid sequence designing apparatus 100 determines the base sequence of siRNA according to the above flow.

FIG. 8 is a diagram showing a data flow of the nucleic acid sequence design process in the first embodiment.
The data flow of the nucleic acid sequence design process in the first embodiment will be described with reference to FIG.

  Based on the base sequence of the mRNA of the target species stored in the type information sequence storage unit 181, the base sequence of the target gene mRNA, the base sequence of the non-target gene mRNA, and the siRNA candidate sequence are acquired (S 501).

  An activity score is calculated based on the base sequence of the target gene mRNA, the base sequence of the non-target gene mRNA, and the inhibition correlation value for the siRNA candidate sequence stored in the inhibition correlation value storage unit 191 (S502).

Based on the siRNA candidate sequence, the base sequence of the mRNA of the non-target gene, the inhibition correlation value for siRNA stored in the inhibition correlation value storage unit 191, and the weighted information value of the gene stored in the gene information storage unit Calculate the score.
Further, the base sequence of siRNA is determined based on the activity score and the influence score (S403).

  In the first embodiment, the nucleic acid sequence design device 100 determines the base sequence of siRNA as described above.

In the first embodiment, the type sequence acquisition unit 210 acquires the mRNA base sequence of the target species from the type information sequence storage unit 181 provided in the nucleic acid sequence design device 100.
However, the nucleic acid sequence design device 100 may not include the type information sequence storage unit 181, and the type sequence acquisition unit 210 may acquire the mRNA base sequence of the target organism species via a network.
Sources of obtaining the mRNA base sequence of the target species include UniGene, which is a database provided by NCBI (National Center for Biotechnology Information).

In the first embodiment, the nucleic acid sequence design device 100 includes the activity score calculation unit 300 and the influence score calculation unit 400, and the siRNA base sequence is determined based on the activity score and the influence score.
However, the nucleic acid sequence design apparatus 100 includes either the activity score calculation unit 300 or the influence score calculation unit 400, and may determine the base sequence of siRNA based on the value calculated by either of them, or other The base sequence of siRNA may be determined in consideration of the value.

Embodiment 2. FIG.
In the first embodiment, the case has been described in which the siRNA candidate sequence is obtained based on the base sequence of the mRNA of the target gene of the target species.
In the second embodiment, a case where a siRNA candidate sequence is acquired from a storage unit will be described.

FIG. 9 is a configuration diagram of the nucleic acid sequence designing apparatus 100 according to the second embodiment.
The configuration of the nucleic acid sequence design apparatus 100 in the second embodiment will be described with reference to FIG.
Here, a configuration different from the nucleic acid sequence designing apparatus 100 of FIG. 2 in the first embodiment will be described, and the other configurations are the same as those of FIG.

In FIG. 9, the nucleic acid sequence design device 100 includes a function-inhibiting nucleic acid sequence storage unit 183 that stores siRNA candidate sequences.
The function-inhibiting nucleic acid sequence storage unit 183 already stores siRNA candidate sequences that have been confirmed to have a certain function-inhibiting effect through experiments or the like.
The candidate sequence acquisition unit 200 acquires a siRNA candidate sequence from the function-inhibiting nucleic acid sequence storage unit 183.

FIG. 10 is a diagram showing a processing flow of the nucleic acid sequence designing apparatus 100 according to the second embodiment.
The flow of the process of the siRNA base sequence design method performed by the nucleic acid sequence design apparatus 100 according to the second embodiment will be described with reference to FIG.
Here, processing different from that in FIG. 3 in the first embodiment will be described, and other processing is assumed to be the same as that in FIG.

  The candidate sequence acquisition unit 200 acquires the siRNA candidate sequence from the function-inhibiting nucleic acid sequence storage unit 183 (S603).

  Steps S601, S602, S604, S605, and S606 are the same as the processing of S101, S102, S104, S105, and S106 in FIG.

  In the second embodiment, the other contents relating to the nucleic acid sequence design method are the same as those in the first embodiment.

Embodiment 3 FIG.
In the first embodiment, the case has been described in which the base sequence of siRNA is obtained from the base sequence of mRNA of the target organism species that is the same species as the target organism.
In Embodiment 3, a case will be described in which the base sequence of siRNA is obtained from the base sequence of mRNA of a target organism.

FIG. 11 is a configuration diagram of the nucleic acid sequence design device 100 according to the third embodiment.
The configuration of the nucleic acid sequence design apparatus 100 according to Embodiment 3 will be described with reference to FIG.
Here, a configuration different from the nucleic acid sequence designing apparatus 100 of FIG. 2 in the first embodiment will be described, and the other configurations are the same as those of FIG.

  In FIG. 11, the nucleic acid sequence design device 100 stores the base sequence of each gene of the target species separately into the base sequence of an exon that is a genetic information part and the base sequence of an intron that is a non-genetic information part. An area array storage unit 182 is provided.

The candidate sequence acquisition unit 200 includes the following.
A base sequence acquisition unit 220 that acquires a base sequence of a target gene of a target organism.
A region sequence acquisition unit 230 that acquires the base sequences of exons and introns of target genes and non-target genes from the type region sequence storage unit 182.
Based on the homology between the target gene and non-target gene of the target organism acquired by the base sequence acquisition unit 220 and the base sequence of the exon and intron acquired by the region sequence acquisition unit 230, the target of the target organism An information sequence acquisition unit 240 that acquires base sequences of mRNAs of genes and non-target genes.

The base sequence acquisition unit 220 can acquire the base sequences of the target gene and the non-target gene of the target organism by the dideoxy method.
First, a target gene and a non-target gene are amplified by a cloning method in which genes are incorporated into a vector to increase the vector, or a PCR method.
Next, a single-stranded gene is obtained from the amplified target gene and non-target gene.
Next, a complementary strand is synthesized from the obtained single-stranded gene with a primer and a polymerase incorporating deoxynucleotide or dideoxynucleotide.
Complementary strands are extended by deoxynucleotides, stopped by dideoxynucleotides, and by using dideoxynucleotides corresponding to each of the four types of bases A, T, G, and C, the complementary strands are extended to each position of each base. Get the gene.
Each gene having a different length has a different amount of charge, and electrophoresis is performed to distinguish the length of the gene from the difference in mobility of each gene. It can be seen that the corresponding base is located.

  When the gene length is about 1000 bp or more, in order to ensure the accuracy of base sequence determination, the gene is divided into several fragments, the base sequence of each fragment is obtained, and the obtained base sequence is A base sequence of the full length of the gene may be obtained in combination.

  However, the base sequence acquisition unit 220 may acquire the base sequences of the target gene and the non-target gene of the target organism by a method other than the above.

  The process of acquiring the base sequences of the target gene and non-target gene mRNA of the target organism performed by the information sequence acquisition unit 240 will be described below with reference to FIGS. 12, 13, and 14.

FIG. 12 is a diagram showing the contents stored in the type area array storage unit 182 in the third embodiment.
In FIG. 12, the type region sequence storage unit 182 stores the base sequence of each exon and each intron region for each gene such as gene A and gene B.

  The base sequence of exon and intron regions to be memorized is obtained from the base sequence of cDNA reversely transcribed from mRNA transcribed from DNA in the target organism species, and the base sequence of cDNA comprising the region corresponding to exon, exon and It can be obtained by comparing with the base sequence of DNA having a region corresponding to an intron.

FIG. 13 is a diagram showing the structure of mRNA in Embodiment 3.
Regarding gene A in FIG. 12, the relationship between mRNA, exon and intron will be described with reference to FIG.
Gene A comprises first to nth exons and introns.
Exons are genetic information regions, introns are non-genetic information regions, and mRNA transcribed from gene A has genetic information corresponding to exons.
And the base sequence which shows the genetic information equivalent to the exon of mRNA has a different base part for every organism even if it is the same organism species. This different base, that is, a polymorphism of one base is called SNP (Single Nucleotide Polymorphism).
In the case of gene A, the base between GAACG and ATGTG is SNP1 containing A or G, the base between AAGCT and CGTTA is SNP2 containing G or C, and between ACCAT and TTCAG Is SNP3 containing G or C.

  That is, even in the same species, the base sequences of genes and mRNAs are different for each organism.

FIG. 14 is a diagram showing a flow of processing for obtaining the base sequence of mRNA of the target gene of the target organism in the third embodiment.
The base sequence of the target gene of the target organism acquired by the base sequence acquisition unit 220 and the base of the exon region and the intron region of the target gene of the target species acquired from the type region sequence storage unit 182 by the region sequence acquisition unit 230 Based on the sequence, the information sequence acquisition unit 240 will explain the flow of processing for acquiring the base sequence of the mRNA of the target gene of the target organism based on FIG.

  The base sequence of the target gene of the target species acquired by the base sequence acquisition unit 220 and the exon region and the intron region of the target gene of the target species acquired from the type region sequence storage unit 182 by the region sequence acquisition unit 230 The base sequence is input (S701).

Obtain the base sequence part of the target gene of the target species that is homologous to the base sequence of the input exon region and intron region, and further, in the region corresponding to the exon in the base sequence part of the target gene of the target species A base sequence is acquired (S702).
The search for homologous sequences uses the Smith-Waterman method or the like.

  The base sequence of the region corresponding to the acquired exon is bound (S703).

  T in the bonded base sequence is replaced with U (S704).

  The base sequence obtained by the replacement is output as the base sequence of the mRNA of the target gene of the target organism (S705).

  By performing the above process on the non-target gene, the base sequence of the mRNA of the non-target gene of the target organism can be obtained.

FIG. 15 is a diagram showing a data flow of the nucleic acid sequence design process in the third embodiment.
The data flow of the nucleic acid sequence design process in the third embodiment will be described with reference to FIG.
Here, a data flow different from that in FIG. 8 in the first embodiment will be described, and the other data flows are assumed to be the same as those in FIG.

  Based on the base sequence of the exon region and intron region of the gene of the target organism species stored in the type region sequence storage unit 182 and the base sequence of the gene of the target organism, the base sequence of the mRNA of the target gene and the non-target gene The base sequence of siRNA and the siRNA candidate sequence are obtained (S801).

  S802 and S803 are the same as S502 and S503 in FIG.

  In the third embodiment, the other contents relating to the nucleic acid sequence design method are the same as in the first embodiment.

  The nucleic acid sequence design apparatus 100 according to the third embodiment includes the function-inhibited nucleic acid sequence storage unit 183 as in FIG. 9 in the second embodiment, and may obtain siRNA candidate sequences from the function-inhibited nucleic acid sequence storage unit 183. Absent.

In Embodiment 3, the region sequence acquisition unit 230 acquires the base sequences of the exon region and the intron region of the gene of the target species from the type region sequence storage unit 182 provided in the nucleic acid sequence design device 100.
However, the nucleic acid sequence design device 100 does not include the type region sequence storage unit 182, and the region sequence acquisition unit 230 acquires the base sequences of the exon region and the intron region of the gene of the target species via the network. Good.
Sources for obtaining the base sequences of the exon region and intron region of the gene of the target species include a database provided by Ensembl.

In Embodiment 3, by providing the information sequence acquisition unit 240, the base sequence acquisition unit 220, and the region sequence acquisition unit 230, the base sequence of mRNA of each gene of the target organism can be acquired.
Moreover, based on the base sequence of mRNA of each gene of the target organism, siRNA candidate sequences can be obtained and the base sequence of siRNA can be designed.

Embodiment 4 FIG.
In the third embodiment, the case where the base sequence of mRNA of the target organism is acquired based on the base sequence of the gene of the target organism and the base sequence of the exon region and intron region of the gene of the target organism species is described. did.
In Embodiment 4, the base sequence of the mRNA of the target organism based on the base sequence of the gene of the target organism species, the SNP of the target organism species, and the base sequence of the exon region and intron region of the gene of the target organism species The case of acquiring the will be described.

FIG. 16 is a configuration diagram of the nucleic acid sequence design device 100 according to the fourth embodiment.
The configuration of the nucleic acid sequence design apparatus 100 according to Embodiment 4 will be described with reference to FIG.
Here, a configuration different from the nucleic acid sequence designing apparatus 100 of FIG. 11 in the third embodiment will be described, and the other configurations are the same as those of FIG.

  In FIG. 16, the nucleic acid sequence design device 100 includes a type information sequence storage unit 181 that stores a base sequence of a gene of a target species.

The candidate sequence acquisition unit 200 includes the following.
A type sequence acquisition unit 210 that acquires the base sequence of the gene of the target species from the type information sequence storage unit 181.
The different sequence acquisition part 250 which acquires SNP of a target organism.
The base sequences of the target and non-target genes of the target species acquired by the type sequence acquisition unit 210, the SNP of the target organism acquired by the different sequence acquisition unit 250, and the target species acquired by the region sequence acquisition unit 230 A base sequence generation unit 260 that generates the base sequences of the target gene and the non-target gene mRNA of the target organism based on the base sequences of the exon region and the intron region of the target gene and the non-target gene.

The different sequence acquisition unit 250 can acquire the SNP of the target organism by genotyping.
A gene containing SNP is amplified by PCR, and the mass of this gene is measured by applying this gene to a mass spectrometer of the type called MALDI-TOF MS, and the base of SNP is A, G by the obtained mass. , C, or T.
Since A, G, C, and T have different masses, the mass of a gene when SNP is A, G, C, or T is measured in advance. A method is possible.

The genotyping performed by the different sequence acquisition unit 250 is not limited to a method using MALDI-TOF MS, but may be an Invader method, a TaqMan method, a SnapShot method, or the like.
Moreover, the method by which the different sequence acquisition unit 250 acquires the SNP of the target organism is not limited to genotyping, and may be a sequence method, an SSCP method, a method using a microarray, or the like.

FIG. 17 is a diagram showing an outline of base sequence generation processing of the base sequence generation unit 260 in the fourth embodiment.
The outline of the process of generating the base sequence of the gene of the target organism performed by the base sequence generation unit 260 in the fourth embodiment will be described with reference to FIG.

SNP1 of gene A of the target organism acquired by the different sequence acquisition unit 250 is G, SNP2 is G, and SNP3 is C, and the gene of the target species acquired by the type sequence acquisition unit 210 from the type information sequence storage unit 820 The base sequence of A is assumed to be: GAACGxATTGTG ... AAGCTxCGTTA ... ACCATxTTCAG ...
In this case, the base sequence generation unit 260 generates the base sequence of the gene A of the target organism as... GAACGGATTGTG... AAGCTGCGTTA ... ACCATCTTCAG.

SNP1 of gene A of the target organism acquired by the different sequence acquisition unit 250 is G, SNP2 is C, SNP3 is C, and the gene of the target species acquired by the type sequence acquisition unit 210 from the type information sequence storage unit 820 The base sequence of A is assumed to be: GAACGxATTGTG ... AAGCTxCGTTA ... ACCATxTTCAG ...
In this case, the base sequence generation unit 260 generates the base sequence of the gene A of the target organism as ... GAACGGATTGTG ... AAGCTCCGTTA ... ACCATCTTCAG ...

  The base sequence generation unit 260 generates the target gene and non-target gene base sequences of the target organism and the target gene and non-target gene exons acquired by the region sequence acquisition unit 230 as described above. Based on the base sequence of the region and the intron region, the base sequences of the target gene and non-target gene mRNA of the target organism are acquired in the same manner as the information sequence acquisition unit 240 in the third embodiment.

FIG. 18 is a diagram showing a data flow of the nucleic acid sequence design process in the fourth embodiment.
The data flow of the nucleic acid sequence design process in the fourth embodiment will be described with reference to FIG.
Here, a data flow different from that in FIG. 15 in the third embodiment will be described, and the other data flows are assumed to be the same as those in FIG.

  The base sequence of the gene of the target species stored in the type information sequence storage unit 181; the base sequence of the exon region and intron region of the gene of the target species stored in the type region sequence storage unit 182; and the base sequence of the target organism Based on the SNP, the base sequence of the target gene mRNA, the base sequence of the non-target gene mRNA, and the siRNA candidate sequence are obtained (S901).

  S902 and S903 are the same as S802 and S803 of FIG.

  In the fourth embodiment, the other contents relating to the nucleic acid sequence design method are the same as those in the third embodiment.

  The nucleic acid sequence design apparatus 100 according to the fourth embodiment includes the function-inhibited nucleic acid sequence storage unit 183 as in FIG. 9 in the second embodiment, and even if siRNA candidate sequences are acquired from the function-inhibited nucleic acid sequence storage unit 183. I do not care.

In Embodiment 4, the type sequence acquisition unit 210 acquires the base sequence of the gene of the target species from the type information sequence storage unit 181 provided in the nucleic acid sequence design device 100.
However, the nucleic acid sequence design device 100 may not include the type information sequence storage unit 181, and the type sequence acquisition unit 210 may acquire the base sequence of the gene of the target organism species via a network.

  In the fourth embodiment, by providing the different sequence acquisition unit 250 and the base sequence generation unit 260, it is possible to reduce the time and cost for acquiring the base sequence of each gene of the target organism.

Embodiment 5. FIG.
In the above embodiment, the mRNA base sequence and siRNA candidate sequence of each gene of the target organism species or target organism are acquired, the activity score for the target gene of the acquired siRNA candidate sequence, and the non-simplification of the acquired siRNA candidate sequence. The nucleic acid sequence design apparatus 100 that calculates the influence score for the target gene and designs the base sequence of siRNA based on the calculated activity score and influence score has been described.
In the fifth embodiment, a function inhibition effect calculation device 600 that calculates an activity score as a function inhibition effect will be described.

FIG. 19 is a configuration diagram of the function inhibition effect calculation device 600 according to the fifth embodiment.
The configuration of the function inhibition effect calculation device 600 according to Embodiment 5 will be described with reference to FIG.

The function inhibition effect calculation device 600 includes the following.
An inhibition correlation value storage unit 191 that stores inhibition correlation values for siRNA base sequences.
An activity score calculation unit 300 that calculates an activity score for the base sequence of siRNA that is a target for calculating the function inhibition effect.
The activity score calculation unit 300 inputs the base sequence of the mRNA of the target gene of the target species or the target organism and the base sequence of the siRNA that is the target for calculating the function inhibition effect, and the inhibition correlation with the base sequence of the input siRNA. The value is acquired from the inhibition correlation value storage unit 191.
Furthermore, an activity score is calculated based on the inputted base sequence of mRNA and base sequence of siRNA and the obtained inhibition correlation value.

  Regarding other contents, the activity score calculation unit 300 and the inhibition correlation value storage unit 191 are the same as the activity score calculation unit 300 and the inhibition correlation value storage unit 191 in the above embodiment.

Embodiment 6 FIG.
In the above embodiment, the nucleic acid sequence design device 100 that designs the base sequence of siRNA and the function inhibition effect calculation device 600 that calculates an activity score as the function inhibition effect have been described.
In the sixth embodiment, a function inhibition influence degree calculation device 700 that calculates an influence score as a function inhibition influence degree will be described.

FIG. 20 is a configuration diagram of the function inhibition influence degree calculation device 700 according to the sixth embodiment.
The configuration of the function inhibition influence calculation device 700 according to the sixth embodiment will be described with reference to FIG.

The function inhibition influence degree calculation device 700 includes the following.
A gene information storage unit 192 that stores gene weighting information values.
An influence score calculation unit 400 that calculates an influence score for the base sequence of siRNA that is a calculation target of the function inhibition influence degree.
The influence score calculation unit 400 inputs the base sequence of the mRNA of the non-target gene of the target species or target organism and the base sequence of the siRNA that is the target of calculating the function inhibition influence level, and enters the base sequence of the input mRNA. The weighting information value of the corresponding non-target gene is acquired from the gene information storage unit 192.
Further, an influence score is calculated based on the inputted base sequence of mRNA and base sequence of siRNA and the obtained weighting information value.

  Regarding other contents, the influence score calculation unit 400 and the gene information storage unit 192 are the same as the influence score calculation unit 400 and the gene information storage unit 192 in the above embodiment.

Embodiment 7 FIG.
In the sixth embodiment, the function inhibition influence degree calculating device 700 that calculates the influence score based on the weighting information has been described.
In the seventh embodiment, a function inhibition influence calculation device 700 that calculates an influence score based on weighting information and an inhibition correlation value will be described.

FIG. 21 is a configuration diagram of the function inhibition influence degree calculation device 700 according to the seventh embodiment.
The configuration of the function inhibition influence degree calculation device 700 according to the seventh embodiment will be described with reference to FIG.

The function inhibition influence degree calculation device 700 includes the following.
A gene information storage unit 192 that stores gene weighting information values.
An inhibition correlation value storage unit 191 that stores inhibition correlation values for siRNA base sequences.
An influence score calculation unit 400 that calculates an influence score for the base sequence of siRNA that is a calculation target of the function inhibition influence degree.
The influence score calculation unit 400 inputs the base sequence of the mRNA of the non-target gene of the target organism species or target organism and the base sequence of the siRNA that is the target of calculating the function inhibition influence level.
Further, the weighted information value of the non-target gene corresponding to the input mRNA base sequence is acquired from the gene information storage unit 192, and the inhibition correlation value for the input siRNA base sequence is acquired from the inhibition correlation value storage unit 191. .
Furthermore, an influence score is calculated based on the base sequence of the input mRNA and the base sequence of siRNA, and the obtained weighting information value and inhibition correlation value.

  Regarding other contents, the influence score calculation unit 400, the gene information storage unit 192, and the inhibition correlation value storage unit 191 are the same as the influence score calculation unit 400, the gene information storage unit 192, and the inhibition correlation value storage unit 191 in the above embodiment. It is the same.

FIG. 22 is a diagram showing the appearance of the nucleic acid sequence design device 100, the function inhibition effect calculation device 600, and the function inhibition influence degree calculation device 700 in the above embodiment.
In FIG. 22, the nucleic acid sequence design device 100, the function inhibition effect calculation device 600, and the function inhibition effect calculation device 700 are composed of a system unit 910, a CRT (Cathode Ray Tube) display device 901, a keyboard (K / B) 902, and a mouse 903. , A compact disk device (CDD) 905, a printer device 906, and a scanner device 907, which are connected by a cable.
Furthermore, the nucleic acid sequence design device 100, the function inhibition effect calculation device 600, and the function inhibition effect calculation device 700 are connected to the FAX machine 932 and the telephone 931 with a cable, and also include a local area network (LAN) 942, a web server 941. It is connected to the Internet 940 via

FIG. 23 is a hardware configuration diagram of the nucleic acid sequence design device 100, the function inhibition effect calculation device 600, and the function inhibition influence degree calculation device 700 in the above embodiment.
In FIG. 23, the nucleic acid sequence design device 100, the function inhibition effect calculation device 600, and the function inhibition influence degree calculation device 700 include a CPU (Central Processing Unit) 911 that executes a program. The CPU 911 includes a ROM 913, a RAM 914, a communication board 915, a CRT display device 901, a K / B 902, a mouse 903, an FDD (Flexible Disk Drive) 904, a magnetic disk device 920, a CDD 905, a printer device 906, and a scanner device 907 via a bus 912. Connected with.
The RAM 914 is an example of a volatile memory. The ROM 913, the FDD 904, the CDD 905, the magnetic disk device 920, and the optical disk device are examples of nonvolatile memories. These are examples of a storage device or a storage unit.
The communication board 915 is connected to a FAX machine 932, a telephone 931, a LAN 942, and the like.
For example, the communication board 915, the K / B 902, the scanner device 907, the FDD 904, and the like are examples of the information input unit.
Further, for example, the communication board 915, the CRT display device 901, and the like are examples of the output unit.

Here, the communication board 915 is not limited to the LAN 942 and may be directly connected to the Internet 940 or a WAN (Wide Area Network) such as ISDN. When directly connected to the Internet 940 or a WAN such as ISDN, the nucleic acid sequence design device 100, the function inhibition effect calculation device 600, and the function inhibition influence degree calculation device 700 are connected to the Internet 940 or a WAN such as ISDN. The web server 941 becomes unnecessary.
The magnetic disk device 920 stores an operating system (OS) 921, a window system 922, a program group 923, and a file group 924. The program group 923 is executed by the CPU 911, the OS 921, and the window system 922.

The program group 923 stores a program for executing a function described as “˜unit” in the description of the above embodiment. The program is read and executed by the CPU 911.
In the file group 924, what is described as “determination result”, “calculation result of”, and “processing result of” in the description of the above embodiment is stored as “˜file”.
In addition, the arrow portion of the flowchart described in the description of the above embodiment mainly indicates input / output of data, and for the input / output of the data, the data includes a magnetic disk device 920, an FD (Flexible Disk cartridge), an optical disk, It is recorded on other recording media such as CD (compact disc), MD (mini disc), DVD (Digital Versatile Disk). Alternatively, it is transmitted through a signal line or other transmission medium.

  Moreover, what is described as “˜unit” in the description of the above embodiment may be realized by firmware stored in the ROM 913. Alternatively, it may be implemented by software alone, hardware alone, a combination of software and hardware, or a combination of firmware.

  The program for carrying out the above embodiment uses a recording device using other recording media such as a magnetic disk device 920, FD, optical disc, CD (compact disc), MD (mini disc), DVD (Digital Versatile Disk). May be stored.

The figure which shows the flow of a process of the arrangement | sequence design of siRNA in a prior art. 1 is a configuration diagram of a nucleic acid sequence design device 100 according to Embodiment 1. FIG. FIG. 3 shows a processing flow of the nucleic acid sequence designing apparatus 100 according to the first embodiment. The figure which shows the memory content of the inhibition correlation value memory | storage part 191 in Embodiment 1. FIG. FIG. 5 is a diagram showing a flow of activity score calculation processing based on an index in the first embodiment. FIG. 5 is a diagram showing a flow of influence score calculation processing in the first embodiment. FIG. 4 shows a flow of siRNA base sequence determination processing in the first embodiment. FIG. 3 shows a data flow of nucleic acid sequence design processing in Embodiment 1. FIG. 3 is a configuration diagram of a nucleic acid sequence design device 100 according to a second embodiment. The figure which shows the flow of a process of the nucleic acid sequence design apparatus 100 in Embodiment 2. FIG. FIG. 6 is a configuration diagram of a nucleic acid sequence design device 100 according to a third embodiment. FIG. 14 is a diagram showing storage contents of a type area array storage unit 182 in the third embodiment. FIG. 5 shows the structure of mRNA in Embodiment 3. The figure which shows the flow of the acquisition process of the base sequence of mRNA of the target gene of the target organism in Embodiment 3. FIG. FIG. 10 shows a data flow of nucleic acid sequence design processing in Embodiment 3. FIG. 6 is a configuration diagram of a nucleic acid sequence design device 100 according to a fourth embodiment. The figure which shows the process outline | summary of the base sequence production | generation of the base sequence production | generation part 260 in Embodiment 4. FIG. FIG. 10 shows a data flow of nucleic acid sequence design processing in Embodiment 4. FIG. 10 is a configuration diagram of a function inhibition effect calculation device 600 according to a fifth embodiment. The block diagram of the function inhibition influence degree calculation apparatus 700 in Embodiment 6. FIG. FIG. 10 is a configuration diagram of a function inhibition influence degree calculation device 700 according to a seventh embodiment. The figure which shows the external appearance of the nucleic acid sequence design apparatus 100, the function inhibition effect calculation apparatus 600, and the function inhibition influence degree calculation apparatus 700 in the said embodiment. The hardware block diagram of the nucleic acid sequence design apparatus 100, the function inhibition effect calculation apparatus 600, and the function inhibition influence calculation apparatus 700 in the said embodiment.

Explanation of symbols

  100 nucleic acid sequence design device, 181 type information sequence storage unit, 182 type region sequence storage unit, 183 function inhibition nucleic acid sequence storage unit, 191 inhibition correlation value storage unit, 192 gene information storage unit, 200 candidate sequence acquisition unit, 210 type sequence Acquisition unit, 220 base sequence acquisition unit, 230 region sequence acquisition unit, 240 information sequence acquisition unit, 250 different sequence acquisition unit, 260 base sequence generation unit, 300 activity score calculation unit, 400 influence score calculation unit, 500 inhibitory sequence determination unit , 600 function inhibition effect calculation device, 700 function inhibition effect calculation device, 901 CRT display device, 902 K / B, 903 mouse, 904 FDD, 905 CDD, 906 printer device, 907 scanner device, 910 system unit, 911 CPU, 912 bus, 913 ROM, 914 RA , 915 communication board, 920 a magnetic disk device, 921 OS, 922 Window system, 923 Program group, 924 File group, 931 telephone, 932 FAX machine, 940 Internet, 941 web server, 942 LAN.

Claims (36)

In a nucleic acid sequence design apparatus for designing a base sequence of a function-inhibiting nucleic acid that inhibits the function of a target gene of a target organism,
A candidate sequence acquisition unit that inputs data on a gene of a target organism and acquires a candidate of a base sequence of a function-inhibiting nucleic acid based on the data on the input gene;
An activity score calculation unit that calculates an activity score indicating a degree of inhibition of the function of the gene by the base sequence with respect to the base sequence acquired by the candidate sequence acquisition unit;
The base sequence acquired by the candidate sequence acquisition unit, an impact score calculation unit that calculates an impact score indicating the degree of influence that inhibits the function of the non-target gene; and
Based on the activity score calculated by the activity score calculation unit and the influence score calculated by the influence score calculation unit, the base sequence is determined from the candidate of the base sequence acquired by the candidate sequence acquisition unit, and the determined base sequence is designed An apparatus for designing a nucleic acid sequence, comprising: an inhibitory sequence determination unit that outputs a base sequence. In a nucleic acid sequence design apparatus for designing a base sequence of a function-inhibiting nucleic acid that inhibits the function of a target gene of a target organism,
A candidate sequence acquisition unit that inputs data on a gene of a target organism and acquires a candidate of a base sequence of a function-inhibiting nucleic acid based on the data on the input gene;
For the base sequence acquired by the candidate sequence acquisition unit, an activity score indicating the degree to which the base sequence inhibits the function of the gene is calculated based on the types of residues constituting the base sequence and the position in the base sequence An activity score calculating unit,
An inhibitory sequence determination unit that determines a base sequence from candidates of the base sequence acquired by the candidate sequence acquisition unit based on the activity score calculated by the activity score calculation unit and outputs the determined base sequence as a designed base sequence A nucleic acid sequence design apparatus characterized by the above. The nucleic acid sequence design apparatus further comprises:
Inhibits the degree to which a function-inhibiting nucleic acid inhibits the function of a target gene when each residue is present at each position in the base sequence relative to the type of residue constituting the base sequence and the position in the base sequence An inhibition correlation value storage unit for storing the correlation value;
The activity score calculation unit calculates an activity score of a base sequence acquired by the candidate sequence acquisition unit based on an inhibition correlation value stored in an inhibition correlation value storage unit. 2. The nucleic acid sequence design apparatus according to 2. The inhibition correlation value stored by the inhibition correlation value storage unit is data based on a known nucleic acid, which indicates a function-inhibiting nucleic acid whose presence or absence of inhibition of the function against the target gene is known,
F (m, n) represents the inhibition correlation value when residue n is present at position m,
Q (m, n) represents the ratio of the known nucleic acid that inhibits function to the presence of residue n at position m in the known nucleic acid that inhibits function;
P (m, n) indicates the proportion of residue n at position m relative to all known nucleic acids,
F (m, n) = log {Q (m, n) / P (m, n)}
4. The nucleic acid sequence design apparatus according to claim 3, wherein The activity score calculation unit
The presence or absence of four or more consecutive sites for at least one of guanine and cytosine in the base sequence;
GC content indicating the content of guanine and cytosine in the base sequence;
The position of the base sequence relative to the target gene;
The nucleic acid according to claim 1 or 2, wherein the activity score of the base sequence acquired by the candidate sequence acquisition unit is calculated based on at least one of the homology between the non-target gene and the base sequence. Array design device. In a nucleic acid sequence design apparatus for designing a base sequence of a function-inhibiting nucleic acid that inhibits the function of a target gene of a target organism,
A candidate sequence acquisition unit that inputs data on a gene of a target organism and acquires a candidate of a base sequence of a function-inhibiting nucleic acid based on the data on the input gene;
The base sequence acquired by the candidate sequence acquisition unit, an impact score calculation unit that calculates an impact score indicating the degree of influence that inhibits the function of the non-target gene; and
Based on the influence score calculated by the influence score calculation unit, the base sequence is determined from the candidate of the base sequence acquired by the candidate sequence acquisition unit, and the inhibition sequence determination unit outputs the determined base sequence as a designed base sequence A nucleic acid sequence design apparatus characterized by the above. The nucleic acid sequence design apparatus further comprises:
The degree to which a function-inhibiting nucleic acid inhibits the function of a non-target gene when each residue is present at each position in the base sequence relative to the type of residue constituting the base sequence and the position in the base sequence. An inhibition correlation value storage unit for storing the inhibition correlation value;
The said influence score calculation part calculates the influence score of the base sequence which the said candidate sequence acquisition part acquired based on the inhibition correlation value memorize | stored in the inhibition correlation value memory | storage part. 6. The nucleic acid sequence design apparatus according to 6. The inhibition correlation value stored by the inhibition correlation value storage unit is data based on a known nucleic acid, which indicates a function-inhibiting nucleic acid whose presence or absence of inhibition of the function against a non-target gene is known,
F (m, n) represents the inhibition correlation value when residue n is present at position m,
Q (m, n) represents the ratio of the known nucleic acid that inhibits function to the presence of residue n at position m in the known nucleic acid that inhibits function;
P (m, n) indicates the proportion of residue n at position m relative to all known nucleic acids,
F (m, n) = log {Q (m, n) / P (m, n)}
8. The nucleic acid sequence designing apparatus according to claim 7, wherein The impact score calculation unit
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
8. The nucleic acid sequence design device according to claim 7, wherein an influence score of the base sequence acquired by the candidate sequence acquisition unit is calculated based on the inhibition correlation value stored in the inhibition correlation value storage unit. The impact score calculation unit
The influence score of the base sequence acquired by the candidate sequence acquisition unit based on the inhibition correlation value stored in the inhibition correlation value storage unit and the homology between the base sequence of the non-target gene and the base sequence of the function-inhibiting nucleic acid The nucleic acid sequence design apparatus according to claim 7, wherein: The impact score calculation unit
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
The influence score of the base sequence acquired by the candidate sequence acquisition unit based on the inhibition correlation value stored in the inhibition correlation value storage unit and the homology between the base sequence of the non-target gene and the base sequence of the function-inhibiting nucleic acid The nucleic acid sequence design apparatus according to claim 7, wherein: The impact score calculation unit
7. The influence score of the base sequence acquired by the candidate sequence acquisition unit is calculated based on the homology between the base sequence of the non-target gene and the base sequence of the function-inhibiting nucleic acid. Nucleic acid sequence design apparatus. The impact score calculation unit
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
The influence score of the base sequence acquired by the candidate sequence acquisition unit is calculated based on the homology between the base sequence of the non-target gene and the base sequence of the function-inhibiting nucleic acid. The nucleic acid sequence design apparatus described. The candidate sequence acquisition unit
From the storage unit that stores the base sequence related to the gene of the species to which the target organism belongs, as a data related to the gene of the target organism, the type sequence acquisition unit that acquires the genetic information sequence indicating the base sequence of the genetic information,
The said candidate sequence acquisition part acquires the candidate of the base sequence of a function inhibition nucleic acid based on the genetic information sequence which the classification sequence acquisition part acquired, The claim 1 or Claim 2 or Claim 6 characterized by the above-mentioned. Nucleic acid sequence design device. The candidate sequence acquisition unit further includes:
Enter the target gene as data on the gene of the target organism,
A different sequence acquisition unit for acquiring a base sequence of a portion different from the base sequence acquired by the type sequence acquisition unit and the base sequence of a target gene of a target organism;
A base sequence generation unit that generates a base sequence based on the base sequence acquired by the type sequence acquisition unit and the base sequence acquired by the different sequence acquisition unit;
The nucleic acid sequence design apparatus according to claim 14, wherein the candidate sequence acquisition unit acquires a candidate for a base sequence of a function-inhibiting nucleic acid based on the base sequence generated by the base sequence generation unit. The candidate sequence acquisition unit
Enter the target gene as data on the gene of the target organism,
A base sequence acquisition unit for acquiring a base sequence from a target gene of a target organism;
The base sequence of each gene possessed by the species to which the target organism belongs belongs to a genetic information region sequence indicating the base sequence of the genetic information region and a non-genetic information region sequence indicating the base sequence of the non-genetic information region. A type region sequence acquisition unit that acquires a genetic information region sequence and a non-genetic information region sequence for a target gene as data on a gene of a target organism from a storage unit that performs,
Based on the homology between the base sequence acquired by the base sequence acquisition unit and the genetic information region sequence and non-genetic information region sequence acquired by the type region sequence acquisition unit, genetic information is obtained from the base sequence acquired by the base sequence acquisition unit. An information sequence acquisition unit that extracts a region sequence and acquires a genetic information sequence indicating a base sequence of genetic information based on the extracted genetic information region sequence;
The said candidate sequence acquisition part acquires the candidate of the base sequence of a function inhibition nucleic acid based on the genetic information sequence which the information sequence acquisition part acquired, The claim 1 or Claim 2 or Claim 6 characterized by the above-mentioned. Nucleic acid sequence design device. The candidate sequence acquisition unit
The nucleic acid sequence design apparatus according to claim 1, 2 or 6, wherein a candidate of a base sequence of a function-inhibiting nucleic acid is obtained from a storage unit that stores a base sequence candidate of the function-inhibiting nucleic acid. In a nucleic acid sequence design method for designing a base sequence of a function-inhibiting nucleic acid that inhibits the function of a target gene of a target organism,
A candidate sequence acquisition step of inputting data on a gene of a target organism and acquiring a candidate of a base sequence of a function-inhibiting nucleic acid based on the data on the input gene;
An activity score calculating step for calculating an activity score indicating the degree to which the base sequence inhibits the function of the gene with respect to the base sequence acquired in the candidate sequence acquisition step;
An influence score calculation step of calculating an influence score indicating the degree of influence by which the base sequence acquired in the candidate sequence acquisition step inhibits the function of the non-target gene; and
Based on the activity score calculated in the activity score calculation step and the influence score calculated in the influence score calculation step, the base sequence was determined from the candidate of the base sequence acquired in the candidate sequence acquisition step, and the determined base sequence was designed A method for designing a nucleic acid sequence, comprising performing an inhibitory sequence determination step of outputting as a base sequence. In a nucleic acid sequence design method for designing a base sequence of a function-inhibiting nucleic acid that inhibits the function of a target gene of a target organism,
A candidate sequence acquisition step of inputting data on a gene of a target organism and acquiring a candidate of a base sequence of a function-inhibiting nucleic acid based on the data on the input gene;
For the base sequence acquired in the candidate sequence acquisition step, an activity score indicating the degree to which the base sequence inhibits the function of the gene is calculated based on the types of residues constituting the base sequence and the position in the base sequence An activity score calculating step,
Based on the activity score calculated in the activity score calculation step, the candidate sequence acquisition step determines a base sequence from the candidate of the base sequence acquired, and executes the inhibition sequence determination step of outputting the determined base sequence as a designed base sequence A method for designing a nucleic acid sequence, comprising: In a nucleic acid sequence design method for designing a base sequence of a function-inhibiting nucleic acid that inhibits the function of a target gene of a target organism,
A candidate sequence acquisition step of inputting data on a gene of a target organism and acquiring a candidate of a base sequence of a function-inhibiting nucleic acid based on the data on the input gene;
An influence score calculation step of calculating an influence score indicating the degree of influence by which the base sequence acquired in the candidate sequence acquisition step inhibits the function of the non-target gene; and
Based on the influence score calculated in the influence score calculation step, the base sequence is determined from the candidate of the base sequence acquired in the candidate sequence acquisition step, and the inhibition sequence determination step that outputs the determined base sequence as the designed base sequence is executed A method for designing a nucleic acid sequence, comprising:   21. A nucleic acid sequence design program for causing a computer to execute the nucleic acid sequence design method according to claim 18, 19 or 20. In the function inhibition effect calculating apparatus for calculating the degree of inhibition of the function of the gene of the target organism by the function-inhibiting nucleic acid,
When each residue is present at each position of the base sequence with respect to the types of residues constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid, the function-inhibiting nucleic acid An inhibition correlation value storage unit for storing the degree of inhibition of the function as an inhibition correlation value;
The degree to which the input function-inhibiting nucleic acid inhibits the function of the gene based on the input base sequence of the function-inhibiting nucleic acid and the inhibition correlation value stored in the inhibition correlation value storage unit. An activity score calculating unit that calculates an activity score indicating the function inhibition effect calculating device. In the function inhibition effect calculating method for calculating the degree of inhibition of the function of the gene of the target organism by the function-inhibiting nucleic acid,
When each residue is present at each position of the base sequence with respect to the types of residues constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid, the function-inhibiting nucleic acid An inhibition correlation value storing step of storing the degree of inhibition of the function as an inhibition correlation value;
The degree to which the input function-inhibiting nucleic acid inhibits the function of the gene based on the input base sequence of the function-inhibiting nucleic acid and the inhibition correlation value stored in the inhibition correlation value storing step. An activity score calculation step of calculating an activity score indicating the function inhibition effect calculation method.   A function inhibition effect calculation program for causing a computer to execute the function inhibition effect calculation method according to claim 23. In the function inhibition influence calculation device for calculating the degree of inhibition of the function of the non-target gene of the target organism by the function-inhibiting nucleic acid,
A function-inhibiting nucleic acid is non-targeted when each residue is present at each position in the base sequence with respect to the type of residue constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid. An inhibition correlation value storage unit for storing the degree of inhibition of gene function as an inhibition correlation value;
Enter the base sequence of the function-inhibiting nucleic acid,
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
An influence score calculation unit that calculates an influence score indicating a degree of inhibition of the function of the non-target gene based on the inhibition correlation value stored in the inhibition correlation value storage unit. The function inhibition influence degree calculation apparatus characterized by the above-mentioned. In the function inhibition influence calculation device for calculating the degree of inhibition of the function of the non-target gene of the target organism by the function-inhibiting nucleic acid,
Enter the base sequence of the function-inhibiting nucleic acid,
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
Based on the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, an impact score calculation unit is provided that calculates an influence score indicating the degree to which the input function-inhibiting nucleic acid inhibits the function of the non-target gene. The function inhibition influence degree calculation apparatus characterized by the above-mentioned. In the function inhibition influence calculation device for calculating the degree of inhibition of the function of the non-target gene of the target organism by the function-inhibiting nucleic acid,
A function-inhibiting nucleic acid is non-targeted when each residue is present at each position in the base sequence with respect to the type of residue constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid. An inhibition correlation value storage unit for storing the degree of inhibition of gene function as an inhibition correlation value;
Enter the base sequence of the function-inhibiting nucleic acid,
Based on the inhibition correlation value stored in the inhibition correlation value storage unit and the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, the base sequence of the input function-inhibiting nucleic acid determines the function of the non-target gene. A function inhibition influence degree calculation device comprising: an influence score calculation unit that calculates an influence score indicating a degree of inhibition. In the function inhibition influence calculation device for calculating the degree of inhibition of the function of the non-target gene of the target organism by the function-inhibiting nucleic acid,
The function-inhibiting nucleic acid is non-targeted when each residue is present at each position in the base sequence with respect to the types of residues constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid. An inhibition correlation value storage unit for storing the degree of inhibition of gene function as an inhibition correlation value;
Enter the base sequence of the function-inhibiting nucleic acid,
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
Based on the inhibition correlation value stored in the inhibition correlation value storage unit and the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, the base sequence of the input function-inhibiting nucleic acid determines the function of the non-target gene. A function inhibition influence degree calculation device comprising: an influence score calculation unit that calculates an influence score indicating a degree of inhibition. In the function inhibition influence calculation method for calculating the degree of inhibition of the function of a non-target gene of a target organism by a function-inhibiting nucleic acid,
A function-inhibiting nucleic acid is non-targeted when each residue is present at each position in the base sequence with respect to the type of residue constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid. An inhibition correlation value storing step of storing the degree of inhibition of the function of the gene as an inhibition correlation value;
Enter the base sequence of the function-inhibiting nucleic acid,
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
Based on the inhibition correlation value stored in the inhibition correlation value storage step, an influence score calculation step of calculating an influence score indicating the degree to which the base sequence of the input function-inhibiting nucleic acid inhibits the function of the non-target gene is executed. The function inhibition influence degree calculation method characterized by this. In the function inhibition influence calculation method for calculating the degree of inhibition of the function of a non-target gene of a target organism by a function-inhibiting nucleic acid,
Enter the base sequence of the function-inhibiting nucleic acid,
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
Based on the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, an impact score calculation step is performed to calculate an influence score indicating the degree to which the input function-inhibiting nucleic acid inhibits the function of the non-target gene. The function inhibition influence degree calculation method characterized by this. In the function inhibition influence calculation method for calculating the degree of inhibition of the function of a non-target gene of a target organism by a function-inhibiting nucleic acid,
A function-inhibiting nucleic acid is non-targeted when each residue is present at each position in the base sequence with respect to the type of residue constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid. An inhibition correlation value storing step of storing the degree of inhibition of the function of the gene as an inhibition correlation value;
Enter the base sequence of the function-inhibiting nucleic acid,
Based on the inhibition correlation value stored in the inhibition correlation value storage step and the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, the base sequence of the input function-inhibiting nucleic acid determines the function of the non-target gene. The function inhibition influence degree calculation method characterized by performing the influence score calculation process which calculates the influence score which shows the degree to inhibit. In the function inhibition influence calculation method for calculating the degree of inhibition of the function of a non-target gene of a target organism by a function-inhibiting nucleic acid,
A function-inhibiting nucleic acid is non-targeted when each residue is present at each position in the base sequence with respect to the type of residue constituting the base sequence of the function-inhibiting nucleic acid and the position in the base sequence of the function-inhibiting nucleic acid. An inhibition correlation value storing step of storing the degree of inhibition of the function of the gene as an inhibition correlation value;
Enter the base sequence of the function-inhibiting nucleic acid,
The amount of genetic information expressed from a non-target gene when the function of the non-target gene is not inhibited by the function-inhibiting nucleic acid;
At least one of functional importance of non-target genes,
Based on the inhibition correlation value stored in the inhibition correlation value storage step and the homology between the non-target gene and the base sequence of the input function-inhibiting nucleic acid, the base sequence of the input function-inhibiting nucleic acid determines the function of the non-target gene. The function inhibition influence degree calculation method characterized by performing the influence score calculation process which calculates the influence score which shows the degree to inhibit.   A function inhibition influence degree calculation program for causing a computer to execute the function inhibition influence degree calculation method according to claim 29, claim 30, or claim 31 or claim 32. The candidate sequence acquisition unit
Obtains the genetic information sequence indicating the base sequence of the genetic information for the target gene and non-target gene from the storage unit that stores the base sequence related to the gene of the species to which the target organism belongs. A type array acquisition unit
The candidate sequence acquisition unit, based on the genetic information sequence of the target gene acquired by the type sequence acquisition unit, acquires a candidate for a base sequence of a function-inhibiting nucleic acid,
The impact score calculation unit
The influence score is calculated based on the homology between the genetic information sequence of the non-target gene acquired by the type sequence acquisition unit and the base sequence of the function-inhibiting nucleic acid acquired by the candidate sequence acquisition unit. Or the nucleic acid sequence design apparatus of Claim 11 or Claim 12 or Claim 13. The candidate sequence acquisition unit further includes:
Enter target and non-target genes as data on the genes of the target organism,
The base sequence of the target gene acquired by the type sequence acquisition unit, the base sequence of the portion different from the base sequence of the target gene of the target organism, the base sequence of the non-target gene acquired by the type sequence acquisition unit, A different sequence acquisition unit for acquiring a base sequence of a portion different from the base sequence of a non-target gene of a target organism;
Generate the target gene base sequence of the target organism based on the base sequence of the target gene acquired by the type sequence acquisition unit and the base sequence of the different part of the target gene acquired by the different sequence acquisition unit, the type A base sequence that generates a base sequence of a non-target gene of a target organism based on a base sequence of a non-target gene acquired by a sequence acquisition unit and a base sequence of a different part of the non-target gene acquired by a different sequence acquisition unit A generator,
The candidate sequence acquisition unit acquires a candidate for a base sequence of a function-inhibiting nucleic acid based on the base sequence of the target gene generated by the base sequence generation unit,
The impact score calculation unit
The influence score is calculated based on the homology between the base sequence of the non-target gene generated by the base sequence generation unit and the base sequence of the function-inhibiting nucleic acid acquired by the candidate sequence acquisition unit. Nucleic acid sequence design apparatus. The candidate sequence acquisition unit
Enter target and non-target genes as data on the genes of the target organism,
A base sequence acquisition unit for acquiring a base sequence of a target gene from a target gene of a target organism, and acquiring a base sequence of the non-target gene from a non-target gene of the target organism;
The base sequence of each gene possessed by the species to which the target organism belongs belongs to a genetic information region sequence indicating the base sequence of the genetic information region and a non-genetic information region sequence indicating the base sequence of the non-genetic information region. A genetic information region sequence and a non-genetic information region sequence for the target gene as data relating to the gene of the target organism from the storage unit, and a genetic information region sequence and a non-genetic information region sequence for the non-target gene A type region array acquisition unit for acquiring
Based on the homology between the base sequence acquired by the base sequence acquisition unit and the genetic information region sequence and non-genetic information region sequence acquired by the type region sequence acquisition unit, genetic information is obtained from the base sequence acquired by the base sequence acquisition unit. A region sequence is extracted, and based on the extracted genetic information region sequence, an information sequence acquisition unit that acquires a genetic information sequence indicating a base sequence of genetic information for a target gene and a non-target gene,
The candidate sequence acquisition unit acquires a candidate for a base sequence of a function-inhibiting nucleic acid based on the genetic information sequence of the target gene acquired by the information sequence acquisition unit,
The impact score calculation unit
The influence score is calculated based on the homology between the genetic information sequence of the non-target gene acquired by the information sequence acquisition unit and the base sequence of the function-inhibiting nucleic acid acquired by the candidate sequence acquisition unit. Or the nucleic acid sequence design apparatus of Claim 11 or Claim 12 or Claim 13.

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