JP2006113786A - Sequence information extraction apparatus, sequence information extraction method and sequence information extraction program - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To create a link file linking acquired sequence information with a sequence character string by extracting a nucleic acid sequence and an amino acid sequence included in arbitrary text data to acquire the sequence information on the extracted sequences. <P>SOLUTION: In a sequence information extraction apparatus 100, a text input part 110 inputs arbitrary text data. A candidate character string extraction part 130, from character strings included in the text data, extracts at least any candidate character string of a candidate character string of the nucleic acid sequence and a candidate character string of the amino acid sequence. A sequence information acquisition part 150, for the extracted candidate character string, acquires the sequence information on a sequence matching the candidate character string from a database. An information link file creation part 170 creates an information link file linking the extracted candidate character string with the acquired sequence information. <P>COPYRIGHT: (C)2006,JPO&NCIPI

Description

  Sequence information extraction apparatus, sequence information extraction method, and sequence information extraction program in bioinformatics.

In the bio-public database, generally, amino acid or nucleotide sequences and natural language comment sentences (hereinafter referred to as annotations) attached thereto are stored as a set.
In addition, many public databases provide an interface (I / F) capable of performing a search for it via the Internet.
There are two main search methods. One is a homology search in which a sequence is input and a search is performed based on sequence similarity. There are many homology search algorithms and there are many programs that implement them, but a program called BLAST is typical. Biobiological databases that provide I / F for performing BLAST searches via WEB include NCBI (USA, http://www.ncbi.nlm.nih.gov/), DDBJ (Japan, http: // www .Ddbj.nig.ac.jp / Welcome-j.html).
The other search method is a method for keyword search for an input natural language word against an annotation. The two public databases mentioned above also provide a WEB (Web) I / F that performs keyword searches.
A user of a bio public database generally performs a homology search and a keyword search by manually inputting search information using a WEB I / F, and acquires single or plural sequence information. The sequence information is information including an amino acid or nucleotide sequence and an annotation attached thereto.
In addition, there is a method using a medical biology literature database that accumulates literature information on medicine and biology to obtain sequence information. In the medical biology literature database, MEDLINE provided by NLM (National Library of Medicine) is famous, and search can be performed using NCBI's literature search system PubMed.
Hereinafter, in the description regarding the acquisition of sequence information using the bio public database, a medical biology literature database may be used instead of the bio public database.
Although the user's interest may be completed by acquiring the sequence information, the user inputs the acquired sequence information into another analysis program and further analyzes the sequence information.
Since many of these analysis programs do not have a WEB I / F, the user once saves the acquired sequence information in the local environment, and then executes the analysis program in the local environment. This procedure will be described below.

FIG. 1 is a diagram showing a procedure for using a bio-public database in the prior art.
In FIG. 1, (1) a user accesses a WEB page of a bio-public database with a WEB browser (hereinafter referred to as a browser), inputs search information to the WEB I / F, and executes a homology search or a keyword search. .
(2) The bio-public database executes a search, converts the result into HTML (Hyper Text Markup Language), and returns it to the browser of the client PC (Personal Computer) operated by the user.
(3) The user looks at the obtained HTML, determines the necessary sequence information for the character string linked to the sequence information, and on the screen on the character string linked to the sequence information determined to be necessary Move the cursor, select the sequence information by clicking the mouse, etc., and instruct the bio public database to download the selected sequence information through the browser.
(4) The browser acquires the sequence information from the bio-public database, downloads the sequence information to the user's client PC, and stores it as a file.
(5) The user moves the stored file to the analysis server in the local environment and executes a desired analysis program.
(6) The user obtains the result output by the analysis program.
The user repeated the above process to obtain necessary sequence information and analysis results.

The following improvements are made to the above prior art.
First, the data stored in the bio public database is downloaded and a mirror database is constructed in the local environment.
Then, a server program having a WEB I / F for performing a search for it is developed.
The user performs a search using the WEB I / F of the server program instead of the bio public database.
By developing the server program independently, for example, by developing a WEB I / F that allows search results to be input to other analysis programs, the user can move sequence information to the analysis program manually, This eliminates the need to input an analysis program execution command. This procedure will be described below.

FIG. 2 is a diagram showing a procedure for using a bio-public database in the prior art.
In FIG. 2, (1) the server program downloads the sequence information of the bio public database in advance and constructs a local database.
(2) A user accesses a WEB page that is an interface of a server program with a browser, inputs search information to the WEB I / F, and executes a homology search or a keyword search.
(3) The server program executes the search, converts the result into HTML, and returns it to the browser of the client PC operated by the user.
(4) The user looks at the obtained HTML, determines the necessary sequence information for the character string linked to the sequence information, and on the screen on the character string linked to the sequence information determined to be necessary Move the cursor, select sequence information by clicking the mouse, and instruct the server program to execute the analysis program for the sequence information.
(5) The server program receives the sequence information selected by the user and executes the analysis program instructed by the user on the analysis server.
(6) When the execution of the analysis program is finished, the server program acquires the result from the analysis server, converts it into HTML, and returns it to the browser of the client PC.
The user repeated the above process to obtain necessary sequence information and analysis results.

The prior art shown in FIG. 2 has the following advantages over the prior art shown in FIG.
In the prior art shown in FIG. 1, in order to use the search result of the bio public database as the input of the analysis program, it is necessary to manually download the acquired sequence information to the client PC and to move it manually to the analysis server. However, in the prior art shown in FIG. 2, it is automated by a server program.
In the prior art shown in FIG. 1, it is necessary for the user to manually input a command in order to execute the analysis program. In the prior art shown in FIG. 2, this is automated by a server program.
In the prior art shown in FIG. 1, most of the analysis program results obtained by the user are expressed in text. However, in the prior art shown in FIG. 2, since the result of the analysis program is converted into HTML by the server program, a graphical or interactive expression is possible depending on the implementation of the server program.

The prior art shown in FIG. 2 has constructed a mirror site that can download data from a bio-public database locally and search for the data. The data in the bio public database is very large, from several GB (gigabytes) to several hundred GB, and the specifications are still different for each database. Therefore, the construction of the mirror site requires expensive H / W (hardware) and complicated S / W (software).
The WEB I / F of the server program is different from that of the bio-public database due to its functional differences. Therefore, users need to get used to operating a look and feel application that differs from the well-known biopublic database.

  In response to the problem that the construction of a mirror site for a bio public database is expensive and requires complicated processing, a main server that constructs a mirror database for a bio public database and a search server that stores an index file for searching A user performs a search from a search server, and the search server acquires data from a main server using an index file (Patent Document 1).

In addition, there is also a technique that displays the results of a survey on biological data (Patent Document 2).
JP 2002-366553 A Japanese translation of PCT publication No. 2003-509776

  However, in the prior art, in order to obtain sequence information or analyze sequence information, the user can search the nucleic acid sequence or amino acid sequence one by one for the nucleic acid sequence or amino acid sequence for which sequence information is to be obtained. It was necessary to input to the interface.

  In addition, for displaying sequence information and analysis results of sequence information, the sequence information obtained by the user and the analysis results analyzed are stored as files one by one, and the necessary files are searched from the stored files. It was necessary to open it.

  Also, for example, when obtaining sequence information or analyzing sequence information about a nucleic acid sequence or amino acid sequence shown in an arbitrary WEB page or text file, the user visually looks at the WEB page or text file, and the WEB page or text It was necessary to cover the nucleic acid sequences and amino acid sequences shown in the file and to input the covered nucleic acid sequences and amino acid sequences one by one into the search interface.

  The present invention has been made to solve the above-described problems, and an object of the present invention is to enable acquisition of sequence information and analysis of sequence information without a user input to a search interface.

  It is another object of the present invention to allow display of sequence information and display of analysis results of sequence information without the need for the user to store the sequence information file and analysis result file and to search and open the stored file.

  In addition, nucleic acid sequences and amino acid sequences can be extracted from nucleic acid sequences and amino acid sequences shown in arbitrary WEB pages and text files without the user viewing the WEB page or text file or covering the nucleic acid sequences and amino acid sequences. The purpose is to do so.

  The sequence information extraction apparatus of the present invention includes a text input unit for inputting text data, and a character string included in the text data input by the text input unit, and at least a candidate character string for a nucleic acid sequence and a candidate character string for an amino acid sequence. A candidate character string extraction unit that extracts any candidate character string, and a sequence information acquisition unit that acquires sequence information of sequences homologous to the candidate character string from the database with respect to the candidate character string extracted by the candidate character string extraction unit It is characterized by comprising.

  The information processing apparatus further includes an information link file generation unit that generates an information link file that links the candidate character string extracted by the candidate character string extraction unit and the sequence information acquired by the sequence information acquisition unit. .

  Further, the sequence information acquisition unit includes a score determination unit that determines a sequence homology score for the sequence information of the homologous sequences acquired by the sequence information acquisition unit, and the information link file generation unit is extracted by the candidate character string extraction unit An information link file is generated by linking a candidate character string and sequence information of a sequence having a high homology score determined by the score determination unit, which is sequence information acquired by the sequence information acquisition unit.

  Furthermore, for the sequence information acquired by the sequence information acquisition unit, the sequence analysis unit for analyzing the sequence, the candidate character string extracted by the candidate character string extraction unit, and the analysis result analyzed by the sequence analysis unit are linked. And an analysis link file generation unit that generates the analyzed link file.

  Further, the sequence information acquisition unit includes a score determination unit that determines a sequence homology score with respect to the sequence information of the homologous sequences acquired by the sequence information acquisition unit, and the sequence analysis unit includes the sequence of information acquired by the sequence information acquisition unit And a sequence having a high homology score determined by the score determination unit is analyzed.

  The candidate character string extraction unit is configured to determine, as an amino acid sequence candidate character string, a character string obtained by combining characters constituting a nucleic acid sequence with respect to a character string included in the text data input by the text input unit. A candidate character string is extracted by including a candidate character string determination unit that performs determination of at least one of determination of a character string combining characters constituting a sequence as a candidate character string of an amino acid sequence.

  The text input unit inputs a markup language source code as text data, and the candidate character string extraction unit extracts a character string enclosed by tags in the markup language source code input by the text input unit. The character string extraction unit and the character string extracted by the tag character string extraction unit are determined to be a character string that is a combination of characters constituting the nucleic acid sequence as a candidate character string of the nucleic acid sequence, and the characters that constitute the amino acid sequence are A candidate character string is extracted by including a candidate character string determination unit that determines at least one of determination of a combined character string as a candidate character string of an amino acid sequence.

  The sequence information extraction apparatus of the present invention is a markup language source code output from a database, a text input unit that inputs a markup language source code indicating sequence information as text data, and a markup input by the text input unit A source code format determining unit for determining a description format in the language source code, an array information extracting unit for extracting sequence information indicated by the markup language source code based on the description format determined by the source code format determining unit, and an array A sequence analysis unit for analyzing the sequence of the sequence information extracted by the information extraction unit is provided.

  And an analysis link file generation unit that generates an analysis link file that links the sequence information indicated by the markup language source code input by the text input unit and the analysis result analyzed by the sequence analysis unit. Features.

  The sequence information extraction method of the present invention includes a text input step for inputting text data, and at least a candidate character string for a nucleic acid sequence and a candidate character string for an amino acid sequence from a character string included in the text data input in the text input step. A candidate character string extracting step for extracting any candidate character string, and a sequence information acquiring step for acquiring sequence information of sequences homologous to the candidate character string from the database with respect to the candidate character string extracted in the candidate character string extracting step And executing.

  The sequence information extraction method of the present invention is a markup language source code output from a database, a text input step for inputting the markup language source code indicating the sequence information as text data, and a markup input in the text input step Sequence analysis that analyzes the sequence for the sequence information indicated by the markup language source code based on the source code format determination process that determines the description format in the language source code and the description format determined in the source code format determination process And performing the process.

  The sequence information extraction program of the present invention causes a computer to execute the sequence information extraction method.

  According to the present invention, sequence information can be obtained and sequence information can be analyzed without a user input to the search interface.

  Further, it is possible to display the sequence information and display the analysis result of the sequence information without storing the sequence information file and the analysis result file by the user and without searching for and opening the stored file.

  In addition, nucleic acid sequences and amino acid sequences can be extracted from nucleic acid sequences and amino acid sequences shown in arbitrary WEB pages and text files without the user viewing the WEB page or text file or covering the nucleic acid sequences and amino acid sequences. .

Embodiment 1 FIG.
FIG. 3 is a diagram showing a procedure for using the bio-public database in the first embodiment.
In FIG. 3, (1) the sequence information extracting apparatus 100 inputs an HTML source code of a WEB page displayed on the WEB browser 210, and extracts a character string indicating a nucleic acid sequence or an amino acid sequence from the HTML source code.
(2) The sequence information extraction apparatus 100 requests the bio public database 200 for sequence information of the nucleic acid sequence or amino acid sequence indicated by the extracted character string.
(3) The bio-public database 200 returns the sequence information in response to the request from the sequence information extraction apparatus 100.
(4) The sequence information extraction apparatus 100 executes an analysis program with the sequence information returned from the bio-public database 200 as an input, and analyzes the nucleic acid sequence or amino acid sequence to be analyzed extracted from the HTML source code in (1). An HTML source code linked with the result is created and displayed on the WEB browser 210 as a WEB page.
The sequence information extraction apparatus 100 performs the above processing on each nucleic acid sequence and each amino acid sequence included in the HTML source code. This allows the user to obtain the necessary sequence information and analysis results, and also moves the cursor over the character string indicating the nucleic acid sequence or amino acid sequence displayed on the WEB page, and clicks the mouse. You can also refer to the analysis results.

FIG. 4 is a diagram illustrating an appearance of the arrangement information extraction apparatus 100 according to the first embodiment.
In FIG. 4, an array information extraction apparatus 100 includes a system unit 910, a CRT (Cathode Ray Tube) display device 901, a keyboard (K / B) 902, a mouse 903, a compact disk device (CDD) 905, a printer device 906, a scanner device. 907, which are connected by a cable.
Further, the array information extraction apparatus 100 is connected to the FAX machine 932 and the telephone 931 via a cable, and is connected to the Internet 940 via a local area network (LAN) 942 and a web server 941.

FIG. 5 is a hardware configuration diagram of the array information extraction apparatus 100 according to the first embodiment.
In FIG. 5, the sequence information extraction apparatus 100 includes 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 a WAN such as the Internet 940 or ISDN, the sequence information extracting apparatus 100 is connected to a WAN such as the Internet 940 or ISDN, and the web server 941 is 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 programs that execute functions described as “˜units” in the description of the embodiments described below. The program is read and executed by the CPU 911.
In the file group 924, what is described as “determination result of”, “calculation result of”, and “processing result of” in the description of the embodiment described below is stored as “˜file”. Yes.
In addition, the arrow portion of the flowchart described in the description of the embodiment described below mainly indicates input / output of data, and for the input / output of the data, the data is the magnetic disk device 920, FD (Flexible Disk cartridge), It is recorded on other recording media such as an optical disc, CD (compact disc), MD (mini disc), and DVD (Digital Versatile Disk). Alternatively, it is transmitted through a signal line or other transmission medium.

  In addition, what is described as “unit” in the description of the embodiment described below 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.

  In addition, a program that implements the embodiment described below may be stored using a recording device using another recording medium such as a magnetic disk device 920, FD, optical disk, CD, MD, or DVD.

The sequence information extraction apparatus 100 according to Embodiment 1 can perform the following processing including the processing shown in FIG.
(1) Input arbitrary text data, extract a character string indicating a nucleic acid sequence or amino acid sequence contained in the text data, obtain sequence information of the nucleic acid sequence or amino acid sequence, and character string indicating the nucleic acid sequence or amino acid sequence An information link file is created by linking the data and the array information.
(2) Input arbitrary HTML source code, extract the character string indicating the nucleic acid sequence or amino acid sequence from the character string enclosed in the HTML tag of the HTML source code, and obtain the sequence information of the nucleic acid sequence or amino acid sequence Then, an information link file is created by linking the character string indicating the nucleic acid sequence or amino acid sequence and the sequence information thereof.
(3) Input the HTML source code indicating the search result of the sequence information using the bio public database, obtain the sequence information indicated in the HTML source code, analyze the sequence with respect to the sequence information, the sequence information and the analysis result Create an analysis link file that links.
(4) Input arbitrary text data, extract a character string indicating the nucleic acid sequence or amino acid sequence contained in the text data, obtain the sequence information of the nucleic acid sequence or amino acid sequence, and analyze the sequence against the sequence information Then, an analysis link file in which a character string indicating the nucleic acid sequence or amino acid sequence and the analysis result are linked is created.
(5) Input an arbitrary HTML source code, extract a character string indicating the nucleic acid sequence or amino acid sequence from the character string enclosed in the HTML tag of the HTML source code, and obtain the sequence information of the nucleic acid sequence or amino acid sequence Then, the sequence is analyzed with respect to the sequence information, and an analysis link file in which the character string indicating the nucleic acid sequence or the amino acid sequence and the analysis result are linked is created.

FIG. 6 is a configuration diagram of the sequence information extraction apparatus 100 according to the first embodiment.
FIG. 7 is a diagram showing a processing flow of the sequence information extraction method according to the first embodiment.
Processing (1) to (5) of the sequence information extracting apparatus 100 will be described below with reference to FIGS.

  First, (1) input arbitrary text data, extract a character string indicating the nucleic acid sequence or amino acid sequence included in the text data, obtain the sequence information of the nucleic acid sequence or amino acid sequence, and indicate the nucleic acid sequence or amino acid sequence The creation of an information link file in which a character string and its sequence information are linked will be described.

The configuration of the sequence information extraction apparatus 100 will be described with reference to FIG. Here, the components related to the process (1) of the sequence information extraction apparatus will be described.
The storage unit 104 stores various data used by the sequence information extraction device 100 such as text data, HTML source code, sequence information, and link files. In addition, data output from each unit constituting the sequence information extracting apparatus 100 is also stored in the storage unit 104 and becomes input data of each unit.
The browser execution unit 101 displays the HTML source code and the link file stored in the storage unit 104 on the WEB browser 210 as a WEB page.
The editor execution unit 105 displays the text data stored in the storage unit 104 on the text editor 220.
The user I / F unit 103 inputs processing instruction data designated by the user, stores the input processing instruction data in the storage unit 104, and outputs the data to the text input unit 110.
Here, the user I / F unit 103 assumes that processing instruction data indicating acquisition of the sequence information of the nucleic acid sequence and amino acid sequence included in the text data displayed in the text editor 220 is input from the user as follows. To do.
The user I / F unit 103 preferably has a form such as a toolbar provided in the WEB browser 210 or the text editor 220.

The text input unit 110 acquires the text data displayed by the editor execution unit 105 from the storage unit 104 based on the processing command data output from the user I / F unit 103, and uses the acquired text data as input. Further, the input text data is output to the source code format determination unit 120.
The source code format determination unit 120 determines the format of text data output from the text input unit 110 and switches processing.
If the format of the text data is not an HTML source code, the process is switched by outputting the text data to the candidate character string determination unit 131 of the candidate character string extraction unit 130.

The candidate character string extraction unit 130 includes a candidate character string determination unit 131, and extracts a candidate character string of a nucleic acid sequence or a candidate character string of an amino acid sequence from the text data output by the source code format determination unit 120. Further, the extracted candidate character string is output to the sequence information acquisition unit 150.
The candidate character string determination unit 131 extracts a candidate character string of a nucleic acid sequence or a candidate character string of an amino acid sequence from the text data output by the source code format determination unit 120. Further, the extracted candidate character string is output to the sequence information acquisition unit 150.
The candidate character string determination unit 131 converts a character string composed of four characters of A (adenine), T (thymine), G (guanine), and C (cytosine) (hereinafter referred to as DNA constituent characters) into a DNA nucleic acid sequence. As a candidate character string (hereinafter referred to as a DNA candidate character string).
In addition, a character string composed of four characters (hereinafter referred to as RNA constituent characters) of A (adenine), U (uracil), G (guanine), and C (cytosine) is converted into a candidate character string (hereinafter referred to as RNA) of an RNA nucleic acid sequence. As a candidate character string).
A (alanine (Ala)), V (valine (Val)), L (leucine (Leu)), I (isoleucine (Ile)), F (phenylalanine (Phe)), W (tryptophan (Trp)), M (methionine (Met)), P (proline (Pro)), G (glycine (Gly)), Y (tyrosine (Tyr)), S (serine (Ser)), T (threonine (Thr)), C ( Cysteine (Cys)), N (Asparagine (Asn)), Q (Glutamine (Gln)), K (Lysine (Lys)), R (Arginine (Arg)), H (Histidine (His)), D (Aspartic acid) (Asp)), E (glutamic acid (Glu)) 20 character strings (hereinafter referred to as amino acid constituent characters) are converted into amino acid sequence candidate character strings (hereinafter referred to as amino acids). Is extracted as a candidate character string).

For example, a word is extracted from text data by performing morphological analysis, and it is determined whether the extracted word includes a character other than a DNA constituent character. As a result of the determination, a word that does not include a character other than a DNA constituent character Are extracted as DNA candidate character strings.
RNA candidate character strings and amino acid candidate character strings are extracted in the same manner.

In addition, for example, a DNA constituent character is searched for text data, and it is determined whether the next character after the searched character is a DNA constituent character. Is determined as one of DNA constituent characters, and when three or more consecutive DNA constituent characters are detected, the character string is extracted as a DNA candidate character string.
RNA candidate character strings and amino acid candidate character strings are extracted in the same manner.
In this case, the number of consecutive constituent characters is not limited to three and is arbitrary.

The sequence information acquisition unit 150 obtains sequence information of a DNA nucleic acid sequence, an RNA nucleic acid sequence, or an amino acid sequence that is homologous to the candidate character string with respect to the candidate character string output by the candidate character string determination unit 131 of the candidate character string extraction unit 130. Search in bio public database. Furthermore, the retrieved sequence information is acquired and output to the score determination unit 160.
Bio public databases include NCBI, DDBJ, and GenBank.
The sequence information acquisition unit 150 may acquire sequence information from any of NCBI, DDBJ, and GenBank, or may acquire sequence information from other databases. Search processing and sequence information acquisition processing are performed according to the database to be used.
Further, the sequence information acquired by the sequence information acquisition unit 150 may be data indicating the content of the sequence information or link information linked to data indicating the content of the sequence information.
The sequence information output from the sequence information acquisition unit 150 to the score determination unit 160 is a table in which each candidate character string output from the candidate character string extraction unit 130 is associated with each sequence information.

FIG. 8 is a diagram showing the contents of the array information in the first embodiment.
The sequence information acquired from bio public databases such as NCBI, DDBJ, and GenBank includes information as shown in FIG.

Classification includes annotation and sequence.
The annotation is a natural language description added to the sequence or a symbol such as a gene name.
The sequence (Sequence) is a nucleotide or amino acid sequence represented by a character string. The nucleotide indicates a DNA candidate letter or an RNA candidate letter, and the nucleotide sequence is a DNA nucleic acid sequence or an RNA nucleic acid sequence.

The entry id is a unique numerical value that identifies a row of array information represented by an integer.
The praiacc is a representative one of the identification codes represented by character strings and added to the sequence by the bio public database.
The accession is an identification code represented by a character string and added to the sequence by the bio public database. There may be more than one.
“locus” is a symbol representing the position of the sequence on the chromosome represented by a character string.
gi is an identification code represented by an integer and added by GenBank to manage the sequence.
The length is the length of the array expressed as an integer.
strand is the direction of the sequence that is translated in vivo, represented by a character string.
The moltype is an identification code indicating whether the sequence is a base sequence or an amino acid sequence, which is represented by a character string. The base sequence is a DNA nucleic acid sequence or an RNA nucleic acid sequence.
The circular is an identification code indicating a linear array or a circular array represented by a character string.
The division is a symbol indicating the classification of the array, which is represented by a character string.
cdate is the date when the array entry was created.
update is the date when the array entry was updated.
The definition is a natural language descriptive text added to the array represented by a character string.
“keyword” is a set of words that expresses the characteristics of the array, which is represented by a character string.
The source is information such as the species or organ of the organism from which the sequence is collected, represented by a character string.
organism is the species of the organism from which the sequence was collected, represented by a character string.
Taxonomic is the biological classification of the organism from which the sequence was collected, expressed as a string.
Taxid is an identification code that identifies a biological species represented by a character string. It is defined in the taxonomy database (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomichome.html/).
“comment” is an additional natural language descriptive text for the array, represented by a character string.

In addition to the above, the sequence information includes a homology search, that is, a homology score of a homology search using BLAST. This homology score includes E-value, bit score, and% id.
E-value is the probability that the sequence is accidentally present in the collation DB, and the smaller the value, the higher the homology. Usually, it is considered that there is significant homology at E-value <0.001. Hereinafter, the homology score is high when the value is small and the homology is high.
The bit score is obtained by adding the scores of matched character strings. The higher the value, the higher the homology. The value is Log with a base of 2.
% Id is the percentage of matching character strings. Usually, it is said that if the amino acid matches 30% or more, the three-dimensional structure is similar, that is, the biochemical function can be expected to be similar.

In FIG. 6, the score determination unit 160 determines the homology score of the homology search included in the sequence information output from the sequence information acquisition unit 150. Further, the sequence information is output to the process switching unit 106 based on the score determination result.
In the determination of the homology score, when the reference homology score is exceeded, that is, when the homology is high, the candidate character string searched in the bio public database by the sequence information acquisition unit 150 is used as a DNA nucleic acid sequence, an RNA nucleic acid sequence, or an amino acid sequence The determined sequence information is output to the process switching unit 106. Furthermore, when there are a plurality of sequence information of candidate character strings determined as DNA nucleic acid sequences, RNA nucleic acid sequences, or amino acid sequences, the sequence information with the highest homology score may be used as the determination result.
For example, the homology score is determined by setting the reference homology score to E-value <0.001.
Alternatively, the E-value, the bit score, and% id may be multiplied by an arbitrary coefficient, and the homology score may be determined based on the total value thereof.

The process switching unit 106 acquires the processing command data input by the user I / F unit 103 from the storage unit 104, and switches processing based on the processing command data.
When the processing instruction data indicates acquisition of sequence information, the sequence information output by the score determination unit 160 is output to the information link file generation unit 170 to switch processing.

The information link file generation unit 170 acquires the processing command data input by the user I / F unit 103 from the storage unit 104, and based on the acquired processing command data and the sequence information output by the processing switching unit 106, the link file And the generated link file is stored in the storage unit 104.
For example, when the processing instruction data indicates acquisition of sequence information of a nucleic acid sequence or amino acid sequence included in the text data displayed in the text editor 220, the text data displayed in the text editor 220 is acquired from the storage unit 104. make a copy.
Further, an HTML source code is generated by inserting a header tag into the copied text data.
Furthermore, the candidate character string output by the candidate character string extraction unit 130 is searched from the generated HTML source code, and the array of sequences determined by the score determination unit 160 as having high homology to the candidate character string searched by the HTML source code A tag linked with information is inserted into the generated HTML source code.

For example, the sequence information acquisition unit 150 outputs a table associating the acquired sequence information with the candidate character string output from the candidate character string extraction unit 130 to the score determination unit 160 as sequence information, thereby generating an information link file The unit 170 can generate an HTML source code, which is an information link file, from the sequence information output from the process switching unit 106 by the process as described above.
Further, the candidate character string extraction unit 130 outputs a table associating the extracted candidate character string with a pointer indicating the position of the candidate character string in the text data to the sequence information acquisition unit 150 as a candidate character string. The information link file generation unit 170 may insert a tag that links the array information at the text data position indicated by the pointer.
Regarding the link of the sequence information to the candidate character string, a tag may be inserted using the address of the WEB page of the sequence information provided by the bio public database 200 as link information.
Further, the sequence information acquisition unit 150 acquires sequence information from the WEB page of sequence information provided by the bio public database 200 and stores the sequence information in the storage unit 104, and the storage position of the sequence information stored in the storage unit 104 is linked information A tag may be inserted as
Alternatively, only the sequence information that the score determination unit 160 has determined to have the highest homology score may be linked, or a plurality of sequence information that the score determination unit 160 has determined to have a homology score that exceeds the reference may be linked. Good.

The processing flow of the sequence information extraction method will be described with reference to FIG. Here, the process (1) of the sequence information extracting apparatus will be described.
First, the following processing is performed in S1.
The user I / F unit 103 inputs processing instruction data designated by the user.
Here, the user I / F unit 103 assumes that processing instruction data indicating acquisition of the sequence information of the nucleic acid sequence or amino acid sequence included in the text data displayed in the text editor 220 is input from the user, and explains the following. To do.
The text input unit 110 inputs the text data displayed on the text editor 220 based on the processing command data input by the user I / F unit 103.
The source code format determination unit 120 determines that the format of the text data input by the text input unit 110 is not an HTML source code, and activates the candidate character string determination unit 131 of the candidate character string extraction unit 130. The text data is input to the candidate character string determination unit 131.
The candidate character string determination unit 131 extracts a DNA candidate character string, an RNA candidate character string, and an amino acid candidate character string from the text data, and stores the extracted candidate character string in the storage unit 104.

Next, in S5, the following processing is performed.
The sequence information acquisition unit 150 refers to the external database for each candidate character string stored in the storage unit 104.
The external database is a bio-public database 200 such as NCBI or DDBJ, and the reference to the external database is to perform homology search or sequence information acquisition.

Next, the following processing is performed in S6.
For each candidate character string, the external database performs a homology search using a nucleic acid database that stores the sequence information of the nucleic acid sequence and an amino acid database that stores the sequence information of the amino acid sequence.
Further, as a result of the homology search, the sequence information of the sequence that is homologous to each candidate character string is returned to the sequence information acquisition unit 150 of the sequence information extraction device 100. The sequence information includes homology scores such as E-value, bit score, and% id.

Next, in S7, the following processing is performed.
The sequence information acquisition unit 150 outputs the sequence information acquired from the external database to the score determination unit 160.
The score determination unit 160 determines a character string indicating a nucleic acid sequence or an amino acid sequence from each candidate character string based on the homology score included in the sequence information.

Next, in S8, the following processing is performed.
The process switching unit 106 determines that the user process instruction data input by the user I / F unit 103 in S1 is acquisition of sequence information, and activates the information link file generation unit 170.

Next, the following processing is performed in S9.
The information link file generation unit 170 acquires link information for the character string in the text data determined by the score determination unit 160 as a nucleic acid sequence or an amino acid sequence from the sequence information acquired by the sequence information acquisition unit 150 from the external database. To do.
Here, the link information acquired from the array information is set as the address of the WEB page indicating the array information provided by the external database. However, it is not limited to the address of the WEB page. For example, the sequence information acquisition unit 150 may store the contents of the sequence information in the storage unit 104, and the storage position of the sequence information in the storage unit 104 may be used as link information.

Next, the following processing is performed in S10.
The information link file generation unit 170 inserts a tag that hyperlinks the acquired link information to the target character string portion of the text data input by the text input unit 110, and generates an HTML source code.
The browser execution unit 101 displays a WEB page indicated by the generated HTML source code on the WEB browser 210.
The user can specify the hyperlink portion of each nucleic acid sequence or each amino acid sequence displayed on the WEB page on the WEB page displayed on the WEB browser 210, and can refer to the respective sequence information.

In the above description, the process (1) of the sequence information extraction apparatus 100 has been described.
Next, (2) an arbitrary HTML source code is input, a character string indicating a nucleic acid sequence or amino acid sequence is extracted from a character string enclosed in an HTML tag of the HTML source code, and the sequence of the nucleic acid sequence or amino acid sequence is extracted. A description will be given of obtaining information and creating an information link file in which a character string indicating a nucleic acid sequence or amino acid sequence is linked to the sequence information.

The configuration of the sequence information extraction apparatus 100 will be described with reference to FIG. Here, regarding the configuration related to the process (2) of the sequence information extraction apparatus 100, a different part from the description of (1) will be described.
The browser execution unit 101 outputs a signal to the signal reception unit 102 when the display of the WEB page on the WEB browser 210 is completed.
The signal receiving unit 102 activates the text input unit 110 when receiving the signal output from the browser execution unit 101.
When activated by the signal receiving unit 102, the text input unit 110 acquires the HTML source code displayed as a WEB page on the WEB browser 210 from the storage unit 104, and inputs the acquired HTML source code as text data. Further, the input text data is output to the source code format determination unit 120.

When the format of the text data output from the text input unit 110 is HTML source code, the source code format determination unit 120 determines whether the WEB page indicated by the HTML source code is the WEB page of the sequence information search result provided by the bio public database. To do. As a result of the determination, if it is not the WEB page of the sequence information search result provided by the bio public database, the process is switched by outputting the HTML source code to the tag character string extraction unit 132 of the candidate character string extraction unit 130.
For example, the character string enclosed by the header tag in the HTML source code which shows the WEB page of the sequence information search result which each biopublic database provides is memorize | stored in the memory | storage part 104, and was enclosed by the header tag in the HTML source code to judge. The determination is performed by comparing the character string and the character string enclosed by the header tag in the HTML source code indicating the WEB page of the sequence information search result provided by each bio public database stored in the storage unit 104.

The candidate character string extraction unit 130 includes a tag character string extraction unit 132 in addition to the candidate character string determination unit 131.
The tag character string extraction unit 132 extracts a character string enclosed by tags in the HTML source code output from the source code format determination unit 120. Further, the extracted character string is output to the candidate character string determination unit 131.
The candidate character string determination unit 131 determines whether the character string output from the tag character string extraction unit 132 is a DNA candidate character string, an RNA candidate character string, or an amino acid candidate character string, and determines the character string determined as one of the candidate character strings. It outputs to the sequence information acquisition part 150 as a candidate character string.
The other parts are the same as the description of the process (1) of the sequence information extraction apparatus 100, the sequence information acquisition unit 150 acquires sequence information, and the information link file generation unit 170 generates an information link file.

The processing flow of the sequence information extraction method will be described with reference to FIG. Here, regarding the processing (2) of the sequence information extracting apparatus 100, a different part from the description of (1) will be described.
First, the following processing is performed in S2.
The browser execution unit 101 starts displaying an arbitrary WEB page on the WEB browser 210, and outputs a signal to the signal receiving unit 102 when the display process ends.
Here, the following explanation will be made assuming that the WEB page displayed on the WEB browser 210 is not the WEB page of the sequence information search result provided by the bio public database.
When receiving a signal, the signal receiving unit 102 activates the text input unit 110.
The text input unit 110 inputs the HTML source code of the WEB page displayed on the WEB browser as text data.
The source code format determination unit 120 determines that the format of the text data input by the text input unit 110 is HTML source code, and is not an HTML source code of the WEB page of the sequence information search result provided by the bio public database. The tag character string extraction unit 132 of the candidate character string extraction unit 130 is activated. The HTML source code is input to the tag character string extraction unit 132.
The tag character string extraction unit 132 extracts a character string enclosed by tags in the HTML source code.

Next, in S4, the following processing is performed.
The candidate character string determination unit 131 extracts a DNA candidate character string, an RNA candidate character string, and an amino acid candidate character string from the character strings extracted by the tag character string extraction unit 132, and stores the extracted candidate character strings in the storage unit 104. Remember.
The subsequent processing is the same as the description of the processing (1) of the sequence information extracting apparatus 100.

In the process (2) of the sequence information extraction apparatus 100, the text input unit 110 inputs the HTML source code in response to a signal indicating that the WEB page has been displayed on the WEB browser output from the browser execution unit 101, and the sequence information is extracted. Started processing.
However, as in the process (1) of the sequence information extraction apparatus 100, the text input unit 110 inputs the HTML source code and starts the sequence information extraction process by the input of the processing instruction data of the user of the user I / F unit 103. Also good.

  Further, although HTML source code is input, other markup language source code may be input without being limited to HTML source code. For example, XML source code may be used.

In the above description, the process (2) of the sequence information extraction apparatus 100 has been described.
Next, (3) HTML source code indicating the search result of the sequence information using the bio public database is input, the sequence information indicated in the HTML source code is acquired, the sequence is analyzed with respect to the sequence information, and the sequence information Creating an analysis link file in which the analysis results are linked to each other will be described.

The configuration of the sequence information extraction apparatus 100 will be described with reference to FIG. Here, regarding the configuration relating to the process (3) of the sequence information extraction apparatus 100, a different part from the description of (1) and (2) will be described.
In the source code format determination unit 120, the format of the text data output from the text input unit 110 is an HTML source code, and the WEB page indicated by the HTML source code is the WEB page of the sequence information search result provided by the bio public database. In this case, it is determined whether the WEB page indicated by the HTML source code is in the format of the WEB page of the sequence information search result provided by any bio-public database. Based on the determined format, any one of the sequence information extraction configuration unit 1411 to the n-th sequence information extraction configuration unit 141n that processes each format of the HTML source code included in the sequence information extraction unit 140 Processing is switched by outputting HTML source code.

  The sequence information extraction unit 140 includes a first sequence information extraction configuration unit 1411 to an n-th sequence information extraction configuration unit 141n and a sequence information editing unit 142, and includes an HTML source code and a bio public database linked from the HTML source code. Extract sequence information from the data. Further, the extracted sequence information is output to the sequence analysis unit 180.

The first sequence information extraction / configuration unit 1411 to the n-th sequence information extraction / configuration unit 141n are respectively in different formats, the HTML source code output from the source code format determination unit 120, and the bio public database data linked from the HTML source code Sequence information is extracted from Further, the extracted sequence information is output to the sequence information editing unit 142.
FIG. 9, FIG. 10, FIG. 11, FIG. 12 and FIG. 13 are diagrams showing the HTML source code format of the WEB page of the bio public database in the first embodiment.
The sequence information extraction method performed by each sequence information extraction component will be described with reference to FIGS.
FIG. 9 is an HTML source code format of Summary display of NCBI Nucleotide / Protein search results.
As for the identification of the WEB page, in the case of Nucleotide search result, the description of “<title> EntrezNucleotide </ title>” in the header tag is determined.
In the case of a Protein search result, the description of “<title> EntrezProtein </ title>” is determined.
The structure of HTML is as shown in FIG. 9 when the description of Java (registered trademark) Script is removed.
By judging DL tag, DT tag, A HREF tag, DD tag, "URL to array" and "Annotation" are extracted, and HTTP request is issued to NCBI using "URL to array" Get an array.

FIG. 10 shows the HTML source code format of FastA display of NCBI Nucleotide search results.
To identify the WEB page, the description of “<TITLE> NCBI Sequence Viewer </ TITLE>” in the header tag is determined.
The structure of HTML is as shown in FIG. 10 when the description of Java (registered trademark) Script is removed.
By determining the PRE tag, “annotation” and “array” are acquired.

FIG. 11 is an HTML source code format of SeqSimpleView display of the SRS search result of DDBJ.
For identifying the WEB page, the description of “<TITLE> Query Result </ TITLE>” in the header tag is determined.
The structure of HTML is as shown in FIG. 11 when descriptions such as Java (registered trademark) Script and unnecessary tag attributes are removed.
By determining the TR tag, TD tag, and A HREF tag, “URL to sequence information” is extracted, and sequence information is acquired from the link destination indicated by “URL to sequence information”.

FIG. 12 is an HTML source code format of FastA display of the SRS search result of DDBJ.
By determining the PRE tag, “annotation” and “array” are acquired.

FIG. 13 shows the HTML source code format of the Complete Entries display of the SRS search result of the DDBJ.
The structure of HTML is as shown in FIG. 13 when descriptions such as Java (registered trademark) Script and unnecessary tag attributes are removed.
By determining the PRE tag, “sequence information” is acquired.

  Similarly, in other WEB pages, the HTML source code format is determined and the sequence information is acquired.

The sequence information editing unit 142 inputs the sequence information acquired by each sequence information extraction configuration unit as described above.
In FIG. 6, the array information editing unit 142 converts the array information acquired from each WEB page into a format independent of the WEB page, and creates array information by combining corresponding arrays. Further, the generated sequence information is output to the sequence analysis unit 180.
For example, the format of the sequence information to be created is set as shown in FIG.

FIG. 14 is a data flow diagram of the sequence information extraction unit 140 in the first embodiment.
In FIG. 14, the text input unit 110 receives an HTML read end signal output from the browser execution unit 101 or a user processing command data input from the user I / F unit 103.
The source code format determination unit 120 is activated from the text input unit 110. Further, the HTML source code of the WEB page displayed on the WEB browser 210 is used as an input.
The first sequence information extraction configuration unit 1411 to the n-th sequence information extraction configuration unit 141n are activated from the source code format determination unit 120. Further, the HTML source code of the WEB page displayed on the WEB browser 210 is used as an input. Also, array information including the array and the annotation is output.
The sequence information editing unit 142 is activated by the first sequence information extraction configuration unit 1411 to the nth sequence information extraction configuration unit 141n. In addition, the sequence information output from the first sequence information extraction configuration unit 1411 to the nth sequence information extraction configuration unit 141n is used as input. The edited sequence information is output.

In FIG. 6, the sequence analysis unit 180 analyzes the sequence information, particularly the sequence included in the sequence information, and outputs the analysis result to the analysis link file generation unit 190.
The analysis process performed by the sequence analysis unit 180 is arbitrary.

The analysis link file generation unit 190 performs the analysis of the sequence analysis unit 180 at the position of the sequence information or the link information to the sequence information in the HTML source code from which the sequence information extraction configuration unit of the sequence information extraction unit 140 has extracted the sequence information. An analysis link file in which the tag to which the result is linked is inserted is generated, and the generated analysis link file is stored in the storage unit 104.
The information to be linked is set as the analysis result of the sequence analysis unit 180, and the generation of the link file is the same as that of the information link file generation unit 170.

  In FIG. 6, the other parts are the same as those in the processes (1) and (2) of the sequence information extracting apparatus 100.

The processing flow of the sequence information extraction method will be described with reference to FIG. Here, regarding the process (3) of the sequence information extraction apparatus 100, a different part from the description of (1) and (2) is demonstrated.
First, the following processing is performed in S3.
The browser execution unit 101 starts displaying an arbitrary WEB page on the WEB browser 210, and outputs a signal to the signal receiving unit 102 when the display process ends.
Here, the WEB page displayed on the WEB browser 210 will be described below assuming that it is a WEB page of the sequence information search result provided by the bio public database.
When receiving a signal, the signal receiving unit 102 activates the text input unit 110.
The text input unit 110 inputs the HTML source code of the WEB page displayed on the WEB browser as text data.
The source code format determination unit 120 determines that the format of the text data input by the text input unit 110 is HTML source code, and further, the HTML source of the WEB page of the sequence information search result provided by any bio public database It is determined that it is a code, and the sequence information extraction configuration unit that processes the HTML source code of the determined WEB page is activated. The HTML source code is used as an input to the sequence information extraction configuration unit.
The sequence information extraction configuration unit extracts sequence information from the HTML source code and the data of the bio public database linked from the HTML source code.
The sequence information editing unit 142 edits the sequence information and stores the edited sequence information in the storage unit 104.

Next, in S11, the following processing is performed.
The sequence analysis unit 180 receives the sequence information stored in the storage unit 104 as input, performs sequence analysis processing, and stores the analysis result in the storage unit 104.

Next, in S12, the following processing is performed.
The analysis link file generation unit 190 acquires the storage position of the analysis result stored in the storage unit 104 as link information.

Next, the following processing is performed in S10.
The analysis link file generation unit 190 inserts a tag that hyperlinks the acquired link information into the target portion of the HTML source code input by the text input unit 110, and generates an HTML source code.
The browser execution unit 101 displays a WEB page indicated by the generated HTML source code on the WEB browser 210.
On the WEB page displayed on the WEB browser 210, the user can specify the hyperlink portion of each nucleic acid sequence or each amino acid sequence displayed on the WEB page, and can refer to the analysis result of each sequence.

In the above description, the process (3) of the sequence information extraction apparatus 100 has been described.
Next, (4) Input arbitrary text data, extract a character string indicating the nucleic acid sequence or amino acid sequence contained in the text data, obtain the sequence information of the nucleic acid sequence or amino acid sequence, and sequence the sequence information Will be described, and an analysis link file in which a character string indicating a nucleic acid sequence or amino acid sequence and an analysis result thereof are linked will be described.

The configuration of the sequence information extraction apparatus 100 will be described with reference to FIG. Here, regarding the configuration relating to the process (4) of the sequence information extracting apparatus 100, a different part from the description of (1) and (3) will be described.
The user I / F unit 103 will be described below assuming that processing instruction data indicating acquisition of the analysis result of the nucleic acid sequence or amino acid sequence included in the text data displayed in the text editor 220 is input from the user.
When the processing instruction data indicates acquisition of the analysis result, the process switching unit 106 outputs the sequence information output by the score determination unit 160 to the sequence analysis unit 180 and switches the process.
The sequence analysis unit 180 analyzes the sequence information, particularly the sequence included in the sequence information, and outputs the analysis result to the analysis link file generation unit 190.
The analysis process performed by the sequence analysis unit 180 is arbitrary.
The analysis link file generation unit 190 generates an analysis link file in which a tag linked to the analysis result of the sequence analysis unit 180 is inserted at a position in the text data of the candidate character string extracted by the candidate character string extraction unit 130, The generated analysis link file is stored in the storage unit 104.
The information to be linked is set as the analysis result of the sequence analysis unit 180, and the generation of the link file is the same as that of the information link file generation unit 170.
In FIG. 6, the other portions are the same as those described in the processes (1) and (3) of the sequence information extraction apparatus 100.

The processing flow of the sequence information extraction method will be described with reference to FIG. Here, regarding the process (4) of the sequence information extraction apparatus 100, a different part from the description of (1) and (3) is demonstrated.
The user I / F unit 103 will be described below assuming that processing instruction data indicating acquisition of the analysis result of the nucleic acid sequence or amino acid sequence included in the text data displayed in the text editor 220 is input from the user.
Processing is performed in the order of S1, S5, S6, and S7, and the processing content is the same as the description of the processing (1) of the sequence information extraction apparatus 100.

Next, in S8, the following processing is performed.
The process switching unit 106 determines that the user process command data input by the user I / F unit 103 in S1 is the acquisition of the analysis result, stores the sequence information in the storage unit 104, and activates the sequence analysis unit 180. To do.

  After the processing of S8, the processing is performed in the order of S11, S12, and S10, and the processing content is the same as the description of the processing (3) of the sequence information extracting apparatus 100.

In the above description, the process (4) of the sequence information extraction apparatus 100 has been described.
Next, (5) an arbitrary HTML source code is input, a character string indicating a nucleic acid sequence or an amino acid sequence is extracted from a character string enclosed in an HTML tag of the HTML source code, and the sequence of the nucleic acid sequence or amino acid sequence is extracted. A description will be given of obtaining information, analyzing the sequence with respect to the sequence information, and creating an analysis link file in which a character string indicating a nucleic acid sequence or an amino acid sequence is linked to the analysis result.

The configuration of the sequence information extraction apparatus 100 will be described with reference to FIG.
The text input unit 110 is activated from the signal receiving unit 102 or the user I / F unit 103 and receives the HTML source code displayed on the WEB browser 210, and the sequence information extraction apparatus 100 reads the nucleic acid sequence included in the HTML source code. Alternatively, an amino acid sequence analysis result is obtained.
The description of each configuration is the same as the description of the process (4) of the sequence information extraction apparatus 100.

The processing flow of the sequence information extraction method will be described with reference to FIG.
The text input unit 110 is activated from the signal receiving unit 102 or the user I / F unit 103 and receives the HTML source code displayed on the WEB browser 210, and the sequence information extraction apparatus 100 reads the nucleic acid sequence included in the HTML source code. Alternatively, an amino acid sequence analysis result is obtained.
The process flow is in the order of S2, S4, S5, S6, S7, S8, S11, S12, and S10, and the contents of the process are the same as those described for the processes (2) and (4) of the sequence information extracting apparatus 100. It is.

  In the first embodiment, the sequence information extraction apparatus 100 can input any text data including HTML source code, so that the user can obtain sequence information or analyze sequence information without input to the bio-public database search interface. Yes.

  In addition, the sequence information extraction apparatus 100 stores the sequence information and the analysis result in the storage unit 104 and can create a link file in which the sequence information and the analysis result are linked to the input text data. Can be displayed and the analysis result of the sequence information can be displayed without the process of searching for the stored file and displaying the searched file.

  In addition, since the nucleic acid sequence or amino acid sequence included in the text data input by the sequence information extraction apparatus 100 can be extracted, the user can visually check the text data and do not cover the nucleic acid sequence or amino acid sequence. Can be extracted.

  In the first embodiment, the link files generated by the information link file generation unit 170 and the analysis link file generation unit 190 are HTML source codes. However, the link files of other markup language source codes are not limited to HTML source codes. It may be generated. For example, XML source code or an editor file format that provides a hyperlink document function may be used.

  In the first embodiment, the homology search is performed using the external database. However, the sequence information extraction apparatus 100 includes a search unit that executes the homology search, the nucleic acid database, and the amino acid database, and does not use the external database. You can do a homology search with.

  In the first embodiment, the sequence information extraction apparatus 100 includes the score determination unit 160 and creates a link file that links sequence information of sequences having high homology scores. However, the head of the homology search result is not performed without performing score determination. You may create the link file which links the arrangement information located in.

Further, if the user I / F unit 103 takes a form such as a toolbar plugged into the WEB browser 210 or the text editor 220, the convenience of the user is improved.
For example, the sequence information extraction apparatus 100 may be configured by a WEB server having a sequence analysis unit 180, a search unit, a nucleic acid database, and an amino acid database, and a plug-in having the configuration of the other sequence information extraction apparatus 100.

For example, a plug-in menu bar may be provided with a user login function and a function for specifying acquired sequence information and analysis information.
FIG. 15 is a diagram illustrating an array information extraction apparatus 100 including a plug-in and a WEB server according to the first embodiment.
The WEB server stores the acquired array information in association with the session ID for identifying the process at the time of acquiring the array information.
The user can access the WEB server by logging in (S2).
The logged-in user can specify a session ID (S1).
In addition, the user can newly request the WEB server to obtain sequence information (S3), and the WEB server generates a unique session ID when receiving a new request (S4).
When a session ID is specified, the WEB server acquires sequence information corresponding to the session ID and performs an analysis process (S5).
The WEB server maps the session ID and the analysis result page (S6), and the plug-in switches the display of the WEB browser 210 to the analysis result page (S7).

The figure which shows the utilization procedure of the bio public database in a prior art. The figure which shows the utilization procedure of the bio public database in a prior art. The figure which shows the utilization procedure of the biopublic database in Embodiment 1. FIG. FIG. 3 shows an external appearance of the sequence information extraction apparatus 100 in the first embodiment. FIG. 3 is a hardware configuration diagram of the sequence information extraction device 100 according to the first embodiment. 1 is a configuration diagram of a sequence information extraction apparatus 100 according to Embodiment 1. FIG. FIG. 5 is a diagram showing a flow of processing of the sequence information extraction method in the first embodiment. FIG. 4 shows the contents of sequence information in the first embodiment. The figure which shows the HTML source code format of the WEB page of the bio public database in Embodiment 1. FIG. The figure which shows the HTML source code format of the WEB page of the bio public database in Embodiment 1. FIG. The figure which shows the HTML source code format of the WEB page of the bio public database in Embodiment 1. FIG. The figure which shows the HTML source code format of the WEB page of the bio public database in Embodiment 1. FIG. The figure which shows the HTML source code format of the WEB page of the bio public database in Embodiment 1. FIG. 3 is a data flow diagram of the sequence information extraction unit 140 in the first embodiment. FIG. 3 is a diagram showing an array information extraction apparatus 100 including a plug-in and a WEB server in the first embodiment.

Explanation of symbols

  DESCRIPTION OF SYMBOLS 100 Sequence information extraction device, 101 Browser execution part, 102 Signal receiving part, 103 User I / F part, 104 Storage part, 105 Editor execution part, 106 Process switching part, 110 Text input part, 120 Source code format determination part, 130 Candidate character string extraction unit, 131 Candidate character string determination unit, 132 Tag character string extraction unit, 140 Sequence information extraction unit, 1411 First sequence information extraction component, 142 Sequence information editing unit, 150 Sequence information acquisition unit, 160 Score determination Unit, 170 information link file generation unit, 180 sequence analysis unit, 190 analysis link file generation unit, 200 bio public database, 210 WEB browser, 220 text editor, 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 RAM, 915 communication board, 920 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 (13)

In a sequence information extraction apparatus connected to a database that stores sequence information of at least one of a nucleic acid sequence and an amino acid sequence,
A text input section for inputting text data;
A candidate character string extraction unit that extracts a candidate character string of at least one of a candidate character string of a nucleic acid sequence and a candidate character string of an amino acid sequence from a character string included in the text data input by the text input unit;
A sequence information extraction apparatus comprising: a sequence information acquisition unit that acquires sequence information of sequences homologous to a candidate character string from a database with respect to the candidate character string extracted by the candidate character string extraction unit. The sequence information extraction device further includes:
The information link file generation unit that generates an information link file that links the candidate character string extracted by the candidate character string extraction unit and the sequence information acquired by the sequence information acquisition unit. The apparatus for extracting sequence information according to 1. The sequence information extraction device further includes:
For the sequence information of the homologous sequences acquired by the sequence information acquisition unit, a score determination unit for determining the sequence homology score,
The information link file generation unit includes a candidate character string extracted by the candidate character string extraction unit, and sequence information of a sequence having a high homology score determined by the score determination unit, which is the sequence information acquired by the sequence information acquisition unit. 3. The sequence information extraction apparatus according to claim 2, wherein a linked information link file is generated. The sequence information extraction device further includes:
For the sequence information acquired by the sequence information acquisition unit, a sequence analysis unit for analyzing the sequence,
2. An analysis link file generation unit that generates an analysis link file that links a candidate character string extracted by the candidate character string extraction unit and an analysis result analyzed by a sequence analysis unit. The sequence information extraction device described. The sequence information extraction device further includes:
For the sequence information of the homologous sequences acquired by the sequence information acquisition unit, a score determination unit for determining the sequence homology score,
5. The sequence information extraction apparatus according to claim 4, wherein the sequence analysis unit analyzes a sequence of information acquired by the sequence information acquisition unit and has a high homology score determined by the score determination unit. The candidate character string extraction unit
The character string included in the text data input by the text input unit is combined with the determination of the character string combining the characters constituting the nucleic acid sequence as the candidate character string of the nucleic acid sequence and the characters constituting the amino acid sequence. The candidate character string is extracted by including a candidate character string determination unit that performs at least one of determination of determining a character string as a candidate character string of an amino acid sequence. The sequence information extraction device described. The text input part
Enter the markup language source code as text data,
The candidate character string extraction unit
A tag character string extraction unit that extracts a character string surrounded by tags in the markup language source code input by the text input unit;
The character string extracted by the tag character string extraction unit is determined as a candidate character string of a nucleic acid sequence that is a combination of characters constituting a nucleic acid sequence, and the character string that is a combination of characters that constitute an amino acid sequence is an amino acid. 6. The array according to claim 1, further comprising: a candidate character string determination unit that performs determination of at least one of determination as a candidate character string of the array, and extracting the candidate character string. Information extraction device. In a sequence information extraction apparatus connected to a database that stores sequence information of at least one of a nucleic acid sequence and an amino acid sequence,
A text input unit for inputting markup language source code indicating sequence information as text data, which is a markup language source code output from a database;
A source code format determination unit for determining a description format in the markup language source code input by the text input unit;
A sequence information extraction unit that extracts sequence information indicated by the markup language source code based on the description format determined by the source code format determination unit;
A sequence information extraction apparatus comprising: a sequence analysis unit that analyzes a sequence of the sequence information extracted by the sequence information extraction unit. The sequence information extraction device further includes:
An analysis link file generation unit that generates an analysis link file that links the sequence information indicated by the markup language source code input by the text input unit and the analysis result analyzed by the sequence analysis unit; The apparatus for extracting sequence information according to claim 8. In a sequence information extraction method of a sequence information extraction apparatus connected to a database that stores sequence information of at least one of a nucleic acid sequence and an amino acid sequence,
A text input process for inputting text data;
A candidate character string extraction step of extracting a candidate character string of at least one of a candidate character string of a nucleic acid sequence and a candidate character string of an amino acid sequence from a character string included in the text data input in the text input step;
A sequence information extraction method comprising: performing a sequence information acquisition step of acquiring sequence information of a sequence homologous to a candidate character string from a database with respect to the candidate character string extracted in the candidate character string extraction step. In a sequence information extraction method of a sequence information extraction apparatus connected to a database that stores sequence information of at least one of a nucleic acid sequence and an amino acid sequence,
A text input process for inputting markup language source code indicating sequence information as text data, which is a markup language source code output from a database;
A source code format determination process for determining a description format in the markup language source code input in the text input process;
A sequence information extraction method comprising: performing a sequence analysis step of analyzing a sequence on sequence information indicated by a markup language source code based on a description format determined in a source code format determination step.   The sequence information extraction program which makes a computer perform the sequence information extraction method of Claim 10 or Claim 11.   10. The sequence information extraction apparatus according to claim 1, wherein the database is at least one of a bio public database and a medical biology literature database.

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