JPH05219932A - Device for examining genetic information - Google Patents

Abstract

PURPOSE:To evaluate the similarity of two amino acid sequences at a high speed in a small volume of the memory by expressing amino acids with letters and evaluating the similarity between the amino acid sequence of an examination target and the amino acid sequence of a reference target. CONSTITUTION:The longest common letter number between an examination target amino acid sequence expressed with a letter sequence and a reference target amino acid sequence expressed with a letter sequence is detected by a detection means 10. The ratio of the longest common letter number to the letter sequence length of the examination target amino acid sequence or reference target amino acid sequence is calculated by a calculation means 11, and the calculated ratio is outputted into an output device 2.

Description

Detailed Description of the Invention

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a genetic information testing apparatus for evaluating the similarity between an amino acid sequence to be tested and an amino acid sequence to be compared, and particularly, the similarity is evaluated according to a simple processing mechanism. The present invention relates to a genetic information testing device that can be used.

In the field of protein engineering required for drug development and the like, a large amount of genetic information has begun to be accumulated with the progress of molecular biology, and a database is now being developed. It is required to extract biologically meaningful information such as protein structure and function from the large amount of accumulated genetic information. It is preferable that the extraction processing is realized by a processing mechanism as simple as possible in order to enable high speed processing.

[0003]

2. Description of the Related Art The main body of a gene is DNA, which is expressed as a base sequence composed of four bases, A (adenine), T (thymine), C (cytosine) and G (guanine). In addition, there are about 20 kinds of amino acids that compose a living body, and it has been clarified so far that the arrangement of three bases in a base sequence corresponds to each amino acid. Therefore, in vivo, an amino acid is synthesized according to the base sequence of DNA, and the synthesized amino acid is folded to form a protein.

As described above, with the development of molecular biology, a method for determining the sequences of bases and amino acids has been established, and a large amount of genetic information such as base sequence data and amino acid sequence data has begun to be accumulated. Therefore, in the field of genetic information processing, from the huge amount of accumulated genetic information,
How to extract biological information about the structure and function of proteins has become a central issue.

The basic method for extracting such biological information is to compare amino acid sequences. This is because similar amino acid sequences are considered to have similar biological functions.

Against this background, in order to estimate the function of the amino acid sequence to be evaluated, a known amino acid sequence database whose function has been elucidated is searched for an amino acid sequence similar to the amino acid sequence to be evaluated. There is a growing tendency to search for homology, and to align amino acid sequences so that differences and similarities between compared amino acid sequences are clear.

[0007] The region of the amino acid sequence which encodes an important function for living organisms is considered to be conserved during evolution. For example, when amino acid sequences of proteins having the same function in different organism species are compared, it is known that there are common sequence patterns. Such a sequence pattern is called a motif. From this, it is possible not only to elucidate the properties and functions of proteins by investigating what kind of motif is contained in the amino acid sequence, but also to strengthen existing proteins, add functions, synthesize new proteins, etc. It can be applied to various fields of protein engineering. From now on, the search for motifs has been started.

Conventionally, as a method of comparing two amino acid sequences, a dynamic programming method used in speech recognition processing or the like has been used.

[0009]

However, in the method for comparing amino acid sequences by the dynamic programming method, since the amino acid sequences are compared two-dimensionally, a large memory capacity is required and a long processing time is required. There was a problem.

The present invention has been made in view of the above circumstances, and is a new gene capable of evaluating the similarity between the amino acid sequence to be examined and the amino acid sequence to be compared according to a simple processing mechanism. It is intended to provide an information inspection device.

[0011]

FIG. 1 (a) shows the principle configuration of the first invention of the present invention, and FIG. 1 (b) shows the principle configuration of the second invention of the present invention.

In FIGS. 1 (a) and 1 (b), reference numeral 1 denotes a genetic information testing apparatus equipped with the present invention, which has a structure in which amino acids are expressed by letters, and has an amino acid sequence to be tested and an amino acid to be compared. The output device connected to the genetic information test device 1 is used to evaluate the similarity with the sequence.

The genetic information testing device 1 of the present invention according to FIG. 1 (a) is a detection device for detecting the maximum number of shared characters between a test amino acid sequence represented by a character string and a comparison target amino acid sequence represented by a character string. The means 10, the calculating means 11 for calculating the ratio of the longest shared character number detected by the detecting means 10, and the character string length of the amino acid sequence to be examined or the amino acid sequence to be compared, and the ratio value calculated by the calculating means 11 are output. Output control means 12 for outputting to the device 2 and calculation means 1
The evaluation unit 13 evaluates the similarity between the test target amino acid sequence and the comparison target amino acid sequence according to the calculated ratio value of 1.

The genetic information testing apparatus 1 of the present invention according to FIG. 1 (b) detects the longest shared subsequence of a test amino acid sequence represented by a character string and a comparison target amino acid sequence represented by a character string. A detection unit 20 and a specifying unit 21 for specifying the sequence position of the longest shared subsequence of the inspection target amino acid sequence and the comparison target amino acid sequence, and for specifying the character string length existing between the sequence positions according to the specifying result. Output control means 22 for outputting the detection result of the detection means 20 and the identification result of the identification means 21 to the output device 2,
The evaluation means 23 evaluates the similarity between the amino acid sequence to be examined and the amino acid sequence to be compared according to the detection result of the detection means 20 and the identification result of the identification means 21.

[0015]

In the genetic information testing apparatus 1 of the present invention according to FIG. 1 (a), for example, when the character string expression of the amino acid sequence to be tested is "ABCBDAB" and the character string expression of the amino acid sequence to be compared is "BDCABA". And the detection means 10
Detects that the maximum number of shared characters in these two character strings is “4”, and the calculation means 11 receives this detection result and uses the character string length of the amino acid sequence to be examined as a reference. 67% when the ratio value of 57% (= 4 ÷ 7) is calculated and the character string length of the comparison target amino acid sequence is used as a reference.
A ratio value of (= 4 ÷ 6) is calculated.

Then, the output control means 12 outputs the calculated ratio value to the output device 2 to inform the user of the similarity between the inspection target amino acid sequence and the comparison target amino acid sequence. The evaluation value is notified, while the evaluation means 1
3 compares the calculated ratio value with a prescribed reference value to mechanically evaluate the similarity between the amino acid sequence to be tested and the amino acid sequence to be compared, and execute the above-mentioned homology test. To go.

As described above, in the genetic information test device 1 of the present invention according to FIG. 1 (a), the maximum number of shared characters between the amino acid sequence to be examined expressed in a character string and the amino acid sequence to be compared in a character string is shared. Is calculated, and the similarity between the amino acid sequence to be tested and the amino acid sequence to be compared is evaluated according to this longest number of shared characters. Therefore, comparison of amino acid sequences by the dynamic programming method is performed. Compared with the method, it is possible to evaluate the similarity between two amino acid sequences with a small memory capacity and at high speed.

In the genetic information test apparatus 1 of the present invention according to FIG. 1 (b), for example, when the character string expression of the amino acid sequence to be tested is "ABCBDAB" and the character string expression of the amino acid sequence to be compared is "BDCABA". And the detection means 2
0 means that the longest shared substring in these two strings is "BDA
B "," BCBA "," BDAB "," BCAB "are detected, and the specifying means 2 receives the detection result.
1 specifies the sequence position of each longest shared partial sequence of the amino acid sequence to be examined and the amino acid sequence to be compared, and also identifies the character string length existing between the sequence positions.

The output control means 22 is the detection means 2
The longest shared subsequence detected by 0 is output as it is, the character string length specified by the specifying unit 21 is output in association with this longest shared subsequence, or the inspection is performed according to the array position specified by the specifying unit 21. By aligning and outputting these two amino acid sequences so that the longest shared subsequences of the target amino acid sequence and the comparison target amino acid sequence are associated with each other, the inspection target amino acid sequence and the comparison target amino acid are presented to the user. Signal the similarity to the sequence.

On the other hand, the evaluation means 23 performs an inspection when the amino acid sequence to be compared is expressed by a continuous character string, or when it is expressed by a character string including an unspecified character string between sequence positions. When evaluating whether or not this comparison target amino acid sequence is included in the target amino acid sequence, the detection means 2 is considered while considering the identification result of the identification means 21.
The above-mentioned motif test is executed by mechanically evaluating whether or not the longest shared subsequence of 0 and the comparison target amino acid sequence match.

As described above, the genetic information test device 1 of the present invention according to FIG. 1 (b) has the longest shared portion between the amino acid sequence to be examined expressed by a character string and the amino acid sequence to be compared expressed by the character string. Since the structure that specifies the sequence is adopted and the similarity between the amino acid sequence to be tested and the amino acid sequence to be compared is evaluated according to this longest shared subsequence, the amino acid sequence of the dynamic programming method Compared with the comparison method, the similarity between two amino acid sequences can be evaluated with a smaller memory capacity and faster.

[0022]

EXAMPLES The present invention will be described in detail below with reference to examples. FIG. 2 illustrates an embodiment of the genetic information test apparatus 1 implementing the present invention. In the figure, 40 is an input device connected to the genetic information test device 1, 41 is an interactive device such as a keyboard or mouse provided in the input device 40, 42 is a display device connected to the genetic information test device 1, and 50 is a character string. An amino acid sequence database that manages the amino acid sequence information represented by, and 60 is a motif database that manages the motif sequence information represented by a character string.

The genetic information test apparatus 1 of this embodiment has the longest distance between the character string of the amino acid sequence input from the input device 40 and the character string of the amino acid sequence provided from the amino acid sequence database 50 or the motif database 60. The number of shared characters and the longest shared substring (LCS: longest
common subsequence) and the LCS detection unit 30 that detects the expanded position of the longest shared subsequence, and the homology that determines the homology between the two amino acid sequences that are the detection targets of the LCS detection unit 30 according to the result of the LCS detection unit 30. The sex determination unit 31,
The homology search unit 32 searches the amino acid sequence database 50 for an amino acid sequence homologous to the amino acid sequence input from the input device 40 according to the detection result of the homology determination unit 31, and the input device according to the result of the LCS detection unit 30. According to the detection results of the LCS detection unit 30 and the motif search unit 33 that searches the motif database 60 for a motif sequence homologous to the amino acid sequence input from 40,
An alignment unit 34 that aligns the character string of the amino acid sequence input from the input device 40 with the character string of the amino acid sequence provided from the amino acid sequence database 50 or the motif database 60, and the display device 42 that displays the processing result of each processing unit. And a display unit 35 for displaying.

Next, the processing executed by the LCS detector 30 will be described in detail according to the processing flows shown in FIGS. Here, the process flow shown in FIG. 3 is a process flow for detecting the maximum number of shared characters of two amino acid sequences to be inspected, and the process flows shown in FIGS. 4 and 5 are to be inspected. It is a processing flow for detecting the longest shared subsequence which one amino acid sequence has, and its expansion position.

When the LCS detection unit 30 detects the maximum number of shared characters between the amino acid sequence represented by the character string 1 and the amino acid sequence represented by the character string 2, it is shown in the processing flow of FIG. As described above, first, in step 1, one character is read from the character string 1 and a table showing the appearance positions of each character in the character string 1 is created.

This appearance table is realized, for example, by connecting the appearance positions of each character with a pointer to an array corresponding to the alphabet from A to Z. For example, the amino acid sequence of the character string 1 is When expressed by "ABCBDAB", as shown in FIG. 6, "A" appears at the 6th and 1st, "B" appears at the 7th, 4th and 2nd, and "C". Appears at the third position, "D" appears at the fifth position, and so on. Then, in this step 1, initialization processing of the array S [i] having the same size as the character string 1 used in the following processing is further executed, and a zero value is set in each entry.

Next, in step 2, one character is read from the character string 2 and the appearance table created in step 1 is referred to,
The appearance position r of the character in the character string 1 is specified. Then, in step 3, it is determined whether the r-th S [r] entry data of the prepared array S [i] is equal to the (r-1) -th S [r-1] entry data. To judge.

When it is judged in this step 3 that S [r] and S [r-1] are equal, the process proceeds to step 4, where the value is equal to or greater than the rth entry data and is equal to the entry data of S [r]. "1" is added to the array S [i] having the entry data, and in the following step 5, it is determined whether or not the processing up to the last character of the character string 2 has been completed, and it is determined that the processing has not been completed. When it does, it returns to step 2. On the other hand, when it is determined in step 3 that S [r] and S [r−1] are not equal, the process immediately proceeds to step 5 without executing the addition process of step 4.

Here, the character string 2 read in step 2
When the character of "1" appears multiple times in the character string 1, the processes of steps 3 and 4 are executed in descending order of the appearance position r.

When it is determined in step 5 that the processing up to the last character of the character string 2 has been completed, the operation proceeds to step 6 and the entry data Kmax of the last element S [m] of the array S [i]. Is output as the maximum number of shared characters.

By executing this processing flow, for example, when the amino acid sequence of the character string 1 is represented by "ABCBDAB" and the amino acid sequence of the character string 2 is represented by "BDCABA", the first character string 2 According to the reading process of the second character B, “r = 7, 4, 2” is specified from the appearance table of FIG. 6, and the entry data of the array S [i] is updated as shown in FIG. According to the reading process of the second character D of the character string 2, "r = 5" is specified from the appearance table of FIG. 6, and the entry data of the array S [i] is updated as shown in FIG. 7B. Then, "r = 3" is specified according to the reading process of the third character C of the character string 2, and the entry data of the array S [i] is updated as shown in FIG. According to the reading process of the fourth character A of No. 2, “r = 6, 1” from the appearance table of FIG. Is specified, the entry data of the array S [i] is updated as shown in Figure 8 (b).

Then, according to the reading process of the fifth character B of the character string 2, "r = 7, 4, 2" is found from the appearance table of FIG.
Is specified, the entry data of the array S [i] is updated as shown in FIG. 9A, and the sixth character A of the character string 2 is updated.
According to the reading process of “r = 6, 1” from the appearance table of FIG.
Is specified, the entry data of the array S [i] is updated as shown in FIG. 9B, and finally, the longest shared character number of "4" is specified. Note that the array S [i] shown in FIGS. 7 to 9 is shown to follow the array S [i] having a size one character larger than the character string 1 for convenience of the system.

Next, with reference to FIGS. 4 and 5, a process for detecting the longest shared partial sequence of two amino acid sequences to be inspected and its expanded position will be described. LC
When the S detection unit 30 detects the longest shared partial sequence between the amino acid sequence represented by the character string 1 and the amino acid sequence represented by the character string 2 and its expanded position, the S detection unit 30 shown in FIG.
As shown in the processing flow of FIG.
Then, one character is read from the character string 1 and a table showing the appearance positions of each character in the character string 1 is created. That is, the appearance table described in FIG. 6 is created. Then, in this step 1, initialization processing of the array S [i] having the same size as the character string 1 used in the following processing is further executed,
An array data [k] that has the same size as the maximum number of shared characters used in the following process, with a zero value set for each entry
Perform the initialization process of to make each entry point to nothing.

Next, in step 11, one character (jth character) is read from the character string 2 and the appearance table created in step 10 is referenced to identify the appearance position r of the character in the character string 1. To do. Then, in step 12, the r-th S [r] entry data of the prepared array S [i] and (r
It is determined whether or not the (-1) th entry data of S [r-1] is equal. When it is determined in step 12 that S [r] and S [r−1] are equal, the process proceeds to step 13,
"1" is added to the array S [i] having the entry data whose value is equal to or greater than the entry data of S [r], which is the r-th,
On the other hand, when it is determined that they are not equal, the process proceeds to step 17 in the process flow of FIG. 5 and the addition process is not executed. Here, when the character of the character string 2 read in step 11 appears multiple times in the character string 1, the processes of step 12 and step 13 are executed in descending order of the appearance position r.

The value k of the entry data of S [r] set in this way is obtained by comparing the character string up to the r-th character of character string 1 and the character string up to the j-th character of character string 2. It becomes the maximum number of shared characters between. In this way, the LCS detector 30
In the case of detecting the longest shared subsequence, the process of detecting the longest shared character number described in the processing flow of FIG. 3 is executed.

When the processing of step 13 is executed, subsequently, in step 14, according to the longest shared character number k which is the entry data of S [r] obtained, the expansion position r in the character string 1 and the character string 2 Paired data (r,
j) is stored in the array data [k]. Here, when the array S [i] has not changed from that in the previous processing cycle, processing is performed so as not to execute this storage processing. The longest shared subsequence is obtained by concatenating this data structure according to the following processing.

Subsequently, moving to the processing flow of FIG. 5, in step 15, the character positions r ', j'stored in data [k-1] are stored.
It is determined whether r '<r, j'<j is satisfied by referring to, and when it is determined that it is satisfied, in response to the fact that the character position is not reversed, the process proceeds to step 16 The position r ′, j ′ is registered as a next candidate by setting a pointer. Then, in the following step 17, it is determined whether or not the processing up to the last character of the character string 2 has been completed. When it is determined that the processing has not been completed, the processing returns to step 11 of the processing flow of FIG. .. On the other hand, when it is determined in step 15 that the above relational expression is not satisfied, the process of step 16 is immediately executed without executing the process of step 16.

When it is determined in step 17 that the processing up to the last character of the character string 2 has been completed, the processing is completed. By executing the processing flows of FIGS. 4 and 5,
As described above, the amino acid sequence of character string 1 is "ABCBD.
It is represented by "AB" and the amino acid sequence of character string 2 is "BDC.
In the case of being represented by “ABA”, “r = 7, 4, 2” is specified from the appearance table of FIG. 6 according to the reading process of the first (j = 1) character B of the character string 2, As shown in FIG. 7A, (7,1) is stored in data [1] by specifying "S [7] = 1" according to "r = 7", and "r =
"S [4] = 1" is specified according to "4"
(4, 1) is stored in [1], and “S =” is entered according to “r = 2”.
When [2] = 1 ”is specified, (2,1) is stored in data [1].

Then, according to the reading process of the second (j = 2) character D of the character string 2, "r =
5 "is specified, and as shown in FIG.
[5] = 2 "is specified and (5,2) is stored in data [2]. Then, according to the reading process of the third (j = 3) character C of character string 2, From the appearance table of 6, "r =
3 ”is identified, and as shown in FIG.
By specifying [3] = 2 ", (3, 3) is stored in data [2]. Then, according to the reading process of the fourth character A (j = 4) of the character string 2, From the appearance table of 6, "r =
6, 1 ”is identified, and as shown in FIG.
By specifying “S [6] = 3” according to “r = 6”,
(6, 4) is stored in data [3], and "S [1] = 1" is specified according to "r = 1".
4) is stored.

Then, in accordance with the reading process of the fifth (j = 5) character B of the character string 2, "r =" from the appearance table of FIG.
7, 4, 2 "is specified, and as shown in FIG. 9A," S [7] = 4 "is specified according to" r = 7 ", so that data [4] has (7, 4, 2). 5) is stored, “S [4] = 3” is specified according to “r = 4”, (4, 5) is stored in data [3], and “S [2] is stored according to“ r = 2 ”. ] =
By specifying "2", (2, 5) is stored in data [2]. Then, the 6th (j = 6) character A of character string 2 is stored.
According to the reading process of “r = 6, 1” from the appearance table of FIG.
Is specified, and as shown in FIG. 9B, “r = 6”
According to the above, “S [6] = 4” is specified, whereby (6, 6) is stored in data [4]. As can be seen from FIG. 9B, since the array S [i] does not change between “r = 6” and “r = 1”, the storage process of (1,6) is not executed.

The character position information (character string 1
And display the expansion position of the same character that character string 2 has),
When the character positions of the data stored in data [k-1] and the data stored in data [k] do not reverse, the pointers are set between them and It is stored in data [k] like.

The longest shared subsequence is specified by tracing the pointer of the character position information stored in this data [k]. That is, to explain using the example of FIG. 10, “(5, 5) of data [4] → (6, 4) of data [3] →
According to the concatenation of (5,2) of data [2] → (4,1) ”of data [1], the longest shared subsequence BDAB and its expansion position in the character string 1 and the character string 2 are specified, and“ data
According to the concatenation of (7, 5) of [4] → (6, 4) of data [3] → (5, 2) of data [2] → (2, 1) of data [1], the longest shared part Column BDAB and character string 1 and character string 2
The expansion position in is identified, and the data (4, (7,
5) → (6,4) of data [3] → (3,3) of data [2] →
According to the concatenation of (2, 1) ”of data [1], the longest shared subsequence BCAB and its expansion position in character string 1 and character string 2 are specified, and (6, 6) → data of“ data [4] → data
According to the concatenation of (4, 5) of [3] → (3, 3) of data [2] → (2, 1) of data [1], the longest shared subsequence BC
The BA and its expanded position in the character string 1 and the character string 2 are specified.

11 and 12, the LCS detector 30 is shown.
However, the processing flow executed when the longest shared subsequence is specified by tracing this connection is illustrated. next,
A process to be executed by each processing unit of the genetic information test apparatus 1 shown in FIG. 2 in response to the longest shared character number detected by the LCS detection unit 30, the longest shared subsequence, and its expanded position will be described. ..

The homology determination unit 31 is supplied from the amino acid sequence database 50 and the motif database 60, together with the character string of the amino acid sequence (hereinafter referred to as the input amino acid sequence) input by the LCS detection unit 30 from the input device 40. When the maximum number of shared characters between the amino acid sequence and the character string is detected, the ratio value between the maximum number of shared characters and the character string length of the input amino acid sequence is detected, and if the ratio value is greater than the specified reference value, Indicates that the input amino acid sequence is the amino acid sequence database 50 or the motif database 60.
It is determined that the amino acid sequence is homologous to the amino acid sequence given by, and if it is smaller than the reference value, it is determined that it is not homologous.

The homology search unit 32 uses the determination result of the homology determination unit 31 to search the amino acid sequence database 50 for an amino acid sequence homologous to the input amino acid sequence.
If there is a homology relationship, the homology determination unit 31
The ratio value calculated by and the longest shared partial sequence detected by the LCS detection unit 30 are displayed on the display device 42 via the display unit 35.

FIG. 13 shows an example of this display example.
This display example shows the results of processing two amino acid sequences of human cytochrome c and bacterial cytochrome c. The longest shared subsequences are arranged in both amino acid sequences at any character intervals. It is configured to display according to the display form indicating whether or not. That is, "GD {x3,3} G {x0,1} K
In the form of displaying {x0,2} ... ", in human cytochrome c, three characters after" GD "are not matched, followed by" G ", and immediately after that," K ". On the other hand, in bacterial cytochrome c, "GD" is followed by three non-matching characters, followed by "G", followed by one non-matching character, and then one It is displayed such that "K" continues.

The motif search unit 33 is a homology determination unit 31.
First, a motif sequence homologous to the input amino acid sequence is searched from the motif database 60 by using the determination result of 1., and subsequently, the longest shared subsequence detected by the LCS detection unit 30 and the sequence position thereof are held. According to the string length and
It is determined whether or not this homologous motif sequence is the original motif sequence. For example, enter a motif sequence called leucine zipper that includes "L" followed by 6 unspecified characters, followed by "L", and the total number of "L" is 5, including up to 6 unspecified characters. Whether or not it is contained in the amino acid sequence is checked according to the detection result of the LCS detection unit 30. And
When the input amino acid sequence has a motif sequence, the motif search unit 33 displays the input amino acid sequence and the motif sequence on the display device 42 via the display unit 35. FIG. 14 illustrates a display example of a rat egg cell potassium channel having a leucine zipper.

The alignment unit 34 includes the LCS detection unit 3
The input amino acid sequence and the amino acid sequence database 5 based on the longest shared subsequence of 0 detected and its expanded position
The two amino acid sequences are aligned and displayed on the display device 42 via the display unit 35 so that the longest shared partial sequence of the amino acid sequence given by 0 or the motif database 60 is associated with each other. FIG. 15 illustrates an example of this display example. This display example displays the processing result of two amino acid sequences of human cytochrome c and bacterial cytochrome c, and the alignment processing is performed by inserting a blank corresponding to the character string length between sequence positions. Will be executed.

[0049]

As described above, according to the present invention,
According to the maximum number of shared characters and the longest shared substring, the maximum number of shared characters and the longest shared subsequence of the amino acid sequence to be examined expressed as a character string and the amino acid sequence to be compared expressed as a character string are detected. Since it has a configuration for evaluating the similarity between the amino acid sequence to be tested and the amino acid sequence to be compared, it has a smaller memory capacity and a higher speed than the method of comparing amino acid sequences by the dynamic programming method. The similarity of two amino acid sequences can be evaluated.

[Brief description of drawings]

FIG. 1 is a principle configuration diagram of the present invention.

FIG. 2 is an example of the present invention.

FIG. 3 is an example of a processing flow executed by an LCS detection unit.

FIG. 4 is an example of a processing flow executed by an LCS detection unit.

FIG. 5 is an example of a processing flow executed by an LCS detection unit.

FIG. 6 is an explanatory diagram of an appearance table created by the LCS detection unit.

FIG. 7 is an explanatory diagram of update processing of the array S [i].

FIG. 8 is an explanatory diagram of an updating process of the array S [i].

FIG. 9 is an explanatory diagram of an updating process of the array S [i].

FIG. 10 is an explanatory diagram of a data structure created by the LCS detection unit.

FIG. 11 is an example of a processing flow executed by an LCS detection unit.

FIG. 12 is an example of a processing flow executed by an LCS detection unit.

FIG. 13 is an example of a display form of processing results.

FIG. 14 is an example of a display form of processing results.

FIG. 15 is an example of a display form of processing results.

[Explanation of symbols]

 DESCRIPTION OF SYMBOLS 1 Gene information test device 2 Output device 10 Detection means 11 Calculation means 12 Output control means 13 Evaluation means 20 Detection means 21 Identification means 22 Output control means 23 Evaluation means

Claims (5)

[Claims] 1. A genetic information test apparatus for evaluating the similarity between an amino acid sequence to be examined and an amino acid sequence to be compared, wherein an amino acid is represented by a character and is represented by a character string. Amino acid sequence to be tested and a detection means (10) for detecting the longest shared character number between the comparison target amino acid sequence represented by a character string, and the longest shared character number detected by the detection means (10),
A genetic information inspection apparatus, comprising: a calculating means (11) for calculating a ratio of the inspection target amino acid sequence or the comparison target amino acid sequence to the character string length. 2. A genetic information test apparatus for evaluating the similarity between an amino acid sequence to be tested and an amino acid sequence to be compared, wherein an amino acid is represented by a character and is represented by a character string. A genetic information testing apparatus comprising a detection means (20) for detecting the longest shared subsequence of a test amino acid sequence and a comparison amino acid sequence represented by a character string. 3. The genetic information test apparatus according to claim 2, further comprising a specifying means (21) for specifying the sequence position of the longest shared partial sequence of the amino acid sequence to be examined and the amino acid sequence to be compared. Genetic information testing device. 4. The genetic information test apparatus according to claim 3, wherein two amino acid sequences are output to an output device, and at the time of output, according to the sequence position specified by the specifying means (21), A genetic information inspection apparatus characterized in that the longest shared subsequences of these two amino acid sequences are aligned and output so that the longest shared subsequences are associated with each other. 5. The genetic information testing apparatus according to claim 3, wherein the longest shared partial sequence of the two amino acid sequences is output to the output device, and at the time of this output, the identifying means is provided.
A genetic information testing device, characterized in that the character string length between the array positions defined according to the array position specified by (21) is processed so as to be output in association with the longest shared character string. ..