Patent Publication Number: US-2020279615-A1

Title: Method of identification, non-transitory computer readable recording medium, and identification apparatus

Description:
CROSS-REFERENCE TO RELATED APPLICATION(S) 
     This application is based upon and claims the benefit of priority of the prior Japanese Patent Application No. 2019-036298, filed on Feb. 28, 2019, the entire contents of which are incorporated herein by reference. 
     FIELD 
     The embodiments discussed herein are related to a method of identification and the like. 
     BACKGROUND 
     In recent years, genomes included in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) of living bodies have been analyzed to predict the influence of new viruses and to develop vaccines and the like. Researches are being conducted that detect gene abnormalities of mutations (point mutations) such as cancer and gene mutations or diagnose the risk of occurrence of diseases based on genomes. 
       FIG. 24  is a diagram for illustrating a genome. This genome  1  is genetic information in which a plurality of amino acids are coupled to each other. The amino acid is determined by a plurality of bases, or a codon. The genome  1  includes a protein  1   a . The protein  1   a  includes a plurality of 20 kinds of amino acids coupled to each other, in which they are coupled to each other like a chain. The structure of the protein  1   a  includes a primary structure, a secondary structure, and a tertiary (a higher order) structure. A protein  1   b  is a protein with the higher order structure. 
     DNA and RNA have four kinds of bases, which are represented by the symbols “A, ” “G,” “C,” and “T,” or “U.” A three-base sequence as a mass determines 20 kinds of amino acids. Each amino acid is represented by the symbols “A” to “Y.”  FIG. 25  is a diagram of a relation among the amino acid, the base, and the codon. A mass of the three-base sequence is called a “codon.” An arrangement of bases determines a codon, and the determined codon determines an amino acid. 
     As illustrated in  FIG. 25 , a plurality of types of codons are associated with one amino acid. Consequently, when the codon is determined, the amino acid is determined, but even when the amino acid is determined, the codon is not uniquely identified. The amino acid. “alanine (Ala)” is associated with the codon “GCU,” “GCC,” “GCA,” or “GCG,” for example. 
     As a technology that searches a genome for certain information, there is a conventional technology that compares base or amino acid sequences by creating an index by the encoding of oligo sequences and searches a database for a specific oligo sequence. Conventional technologies are described in Japanese Laid-open Patent Publication No. 2003-256433 and Japanese Laid-open Patent Publication No. 2004-280614, for example. 
     SUMMARY 
     According to an aspect of an embodiment, a method of identification includes acquiring a protein file in which a plurality of proteins including a plurality of amino acids are arranged, using a processor; identifying a plurality of primary structure candidates with any position included in the protein file as a starting position, using the processor; and identifying one primary structure among the primary structure candidates based on a combination of a primary structure and each amino acid and a primary structure table, where the each amino acid is positioned at an end of the primary structure and the primary structure table associates a primary structure and a cooccurrence rate of a certain amino acid combination positioned at an end of the primary structure, using the processor. 
     The object and advantages of the invention will be realized and attained by means of the elements and combinations particularly pointed out in the claims. 
     It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory and are not restrictive of the invention, as claimed. 
    
    
     
       BRIEF DESCRIPTION OF DRAWINGS 
         FIG 1  is a diagram ( 1 ) for illustrating processing by an identification apparatus according to a first example; 
         FIG. 2  is a diagram ( 2 ) for illustrating the processing by the identification apparatus according to the first example; 
         FIG. 3  is a diagram ( 3 ) for illustrating the processing by the identification apparatus according to the first example; 
         FIG. 4  is a diagram ( 4 ) for illustrating the processing by the identification apparatus according to the first example; 
         FIG. 5  is a functional block diagram of configuration of the identification apparatus according to the first example; 
         FIG. 6  is a diagram of an exemplary data structure of a conversion table; 
         FIG. 7  is a diagram of an exemplary data structure of a codon transposition index; 
         FIG. 8  is a diagram of an exemplary data structure of a protein dictionary; 
         FIG. 9  is a diagram of an exemplary data structure of a protein hidden Markov model (HMM); 
         FIG 10  is a diagram of an exemplary data structure of a protein transposition index; 
         FIG 11  is a diagram for illustrating exemplary processing to hash the codon transposition index; 
         FIG 12  is a diagram for illustrating exemplary processing to identify a protein included in a codon compression file by a cooccurrence totalization unit; 
         FIG 13  is a diagram for illustrating processing to reconstruct the hashed bitmap; 
         FIG 14  is a flowchart of a processing procedure by the identification apparatus according to the first example; 
         FIG 15  is a diagram ( 1 ) for illustrating processing by an identification apparatus according to a second example; 
         FIG 16  is a diagram ( 2 ) for illustrating the processing by the identification apparatus according to the second example; 
         FIG 17  is a diagram ( 3 ) for illustrating the processing by the identification apparatus according to the second example; 
         FIG 18  is a functional block diagram of a configuration of the identification apparatus according to the second example; 
         FIG 19  is a diagram of an exemplary data structure of a primary structure dictionary; 
         FIG. 20  is a diagram of an exemplary data structure of a primary structure HMM; 
         FIG. 21  is a diagram of an exemplary data structure of a primary structure transposition index; 
         FIG. 22  is a flowchart of a processing procedure by the identification apparatus according to the second example; 
         FIG. 23  is a diagram of an exemplary hardware configuration of a computer implementing functions similar to those of the identification apparatuses according to the examples; 
         FIG. 24  is a diagram for illustrating a genome; and 
         FIG. 25  is a diagram of a relation among an amino acid, a base, and a codon. 
     
    
    
     DESCRIPTION OF EMBODIMENTS 
     However, the conventional technologies described above have a problem in that the primary structure of proteins included in the genome is not able to be identified. 
     Information on the genome is various such as information by base, information by codon, or information by amino acid, for example. Conventional technologies are not able to convert the information by amino acid into the information by codon. Given these circumstances, dictionary information or the like with which information on the primary structure of proteins is associated may be created by base, codon, and amino acid, and a comparison between the genome and dictionary information may be performed; an enormous amount of data of the dictionary information reduces the speed of identifying the primary structure. 
     Preferred embodiments of the present invention will be explained with reference to accompanying drawings. These examples do not limit the present invention. 
     [a] First Example 
       FIG 1  to  FIG. 4  are diagrams for illustrating processing by an identification apparatus according to a first example. The following first describes  FIG 1 . A base file  150   a  is a file holding information in which a plurality of bases are arranged. DNA and RNA have four kinds of bases, which are represented by the symbols “A,” “G,” “C,” and “T,” or “U.” 
     A first encoding unit  160   b  of the identification apparatus generates a codon compression file  150   c  and a codon transposition index  150   d  from the base file  150   a  based on a conversion table  150   b.    
     The conversion table  150   b  is a table associating a codon and a codon code with each other. A mass of a three-base sequence is called a “codon.” 
     The first encoding unit  160   b  extracts bases in groups of three from the base file  150   a  and compares the extracted bases and the conversion table  150   b  with each other to identify a code corresponding to three bases (a codon) and converts the three bases (the codon) into the code. The first encoding unit  160   b  repeatedly executes the processing to generate the codon compression file  150   c . The codon compression file  150   c  is information in which codes by codon are arranged. In the first example, bases (a codon) before encoding are represented within parentheses next to a code for the sake of convenience. The codon “AUG” is converted into a code “63h,” for example, in which the converted code is denoted by “(AUG)63h.” The letter “h” indicates that it is a hexadecimal numbers 
     When generating the codon compression file  150   c , the first encoding unit  160   b  generates the codon transposition index  150   d . The codon transposition index  150   d is information associating an offset from the top of the codon compression file  150   c  and a codon type (the codon code) with each other. 
     The following describes  FIG. 2 . A cooccurrence totalization unit  160   c  of the identification apparatus generates a protein hidden Markov model (HMM)  150   f  and a dictionary index  150   g  based on the codon compression file  150   c , the codon transposition index  150   d , and a protein dictionary  150   e.    
     The protein dictionary  150   e  is information associating a protein code and a codon code sequence with each other. The codon code sequence is information in which a plurality of codon codes are arranged combination of codons (codon codes) varies in accordance with the type of the protein, and the number of codons corresponding to the protein varies. 
     The cooccurrence totalization unit  160   c  identifies a codon combination included in the codon compression file  150   c  based on the codon transposition index  150   d . The cooccurrence totalization unit  160   c  repeatedly executes processing to compare the codon combination. (the codon code sequence) and the codon code sequence of the protein dictionary  150   e  with each other to identify protein codes included in the codon compression file  150   c.    
     The cooccurrence totalization unit  160   c , in the process of repeatedly executing the above processing, sets a “break” of the codon code sequence corresponding to each protein included in the codon compression file  150   c  in the dictionary index  150   g . In a codon code sequence “02h63h78h⋅⋅03h02h52h79h⋅03h,” for example, the codon code sequence “02h63h78h⋅⋅03h” is a codon code sequence corresponding to a protein code “8000h,” whereas the codon sequence “02h52h79h⋅03h” is a codon sequence corresponding to a protein code “8001h.” In this case, the gap between the codon code sequences “02h63h78h⋅⋅03h” and “02h52h79h⋅⋅03h” is the “break.” In the dictionary index  150   g , each break is indicated by the offset from the top of the codon compression file  150   c . In the first example, the break is indicated by the offset of a top code of a following codon code sequence as an example. In the above example, the offset of the top code &lt;02h&gt;of the following “02h52h79h⋅⋅03h” is the offset of the break. 
     In the process in which the cooccurrence totalization unit  160   c  performs the above processing, a codon code sequence from a certain offset of the codon compression file  150   c  may match a plurality of codon code sequences having different lengths included in the protein dictionary  150   e.    
     As illustrated in  FIG. 3 , for example, a codon code sequence from an offset P of a certain break of the codon compression file  150   c  to an offset may correspond to the code of a protein A, whereas a codon code sequence from the offset P to an offset N 3  may match the code of a protein B. 
     In this case, the cooccurrence totalization unit  160   c  sets the codon code of offsets P to P+N A  as the code. of the protein A, sets an offset. P+N A +1 as a break, and repeatedly executes the above processing. The cooccurrence totalization unit  160   c  sets the codon code of offsets P to P+N B  as the code of the protein B, sets an offset P+N B +1 as a break, and repeatedly executes the above processing. 
     The cooccurrence totalization unit  160   c  repeatedly executes the above process to totalize the type of a protein code following a certain protein code and to calculate a cooccurrence rate with the certain protein code. It is assumed that the codon code sequence of the protein A has appeared M A  times in the codon compression file  150   c , for example. When the codon code sequence of the protein. B among various kinds of proteins following the codon code sequence of the protein A has appeared L B  times, the cooccurrence rate of the code of the protein A and the code of the protein B is “L B /M A /100.” The cooccurrence totalization unit  160   c  repeatedly executes the processing to calculate the cooccurrence rate for each protein to generate the protein HMM  150   f . The protein HMM  150   f  is information defining each protein pair and the cooccurrence rate. 
     The following describes  FIG. 4 . A second encoding unit  160   d  of the identification apparatus generates a protein compression file  150   h  and a protein transposition index  150   i  based on the codon compression file  150   c , the codon transposition index  150   d , the protein dictionary  150   e , the dictionary index  150   g , and the protein HMM  150   f . The second encoding unit  160   d  is an exemplary “identification unit.” 
     The second encoding unit  160   d  identifies the break of the codon code sequence of each protein included in the codon compression file  150   c  based on the dictionary index  150   g . Based on the codon code sequence between each break and protein dictionary  150   e , the second encoding unit  160   d  identifies the protein code corresponding to the codon code sequence between each break and converts the codon code sequence into the protein code. 
     When the codon code sequence following the protein code (the break) corresponds to a plurality of protein codes, the second encoding unit  160   d  identifies a protein code having the highest cooccurrence rate among the corresponding protein codes based on the protein HMM  150   f . The second encoding unit  160   d  converts the codon code sequence following the break into the identified protein code. The second encoding unit  160   d  repeatedly executes the above processing to generate the protein compression file  150   h.    
     When generating the protein compression file  150   h , the second encoding unit  160   d  generates the protein transposition index  150   i . The protein transposition index  150   i  is information associating an offset from the top of the protein compression file  150   h  and the protein code with each other. 
     As described above, the identification apparatus according to the first example calculates the cooccurrence rate of a protein included in the codon compression file  150   c  and a protein following this protein to generate the protein HMM  150   f . Using the protein HMM  150   f , the identification apparatus can cut out the codon code. sequence of the codon compression file  150   c  in units of correct proteins. Cutting out in units of correct proteins can generate the protein compression file  150   h  with the codon compression file  150   c  encoded in units of proteins. In addition, the sequence of the proteins included in the codon compression file  150   c  can be identified, and the primary structure of the proteins can easily be identified. 
     The following describes an exemplary configuration of an identification apparatus  100  according to the first example.  FIG. 5  is a functional block diagram of a configuration of the identification apparatus according to the first example. As illustrated in  FIG. 5 , this identification apparatus  100  has a communication unit  110 , an input unit  120 , a display unit  130 , a storage unit  150 , and a controller  160 . 
     The communication unit  110  is a processing unit executing data communication with another external apparatus (not illustrated) via a network. The communication unit  110  corresponds to a communication apparatus, for example. The communication unit  110  may receive the base file  150   a  described below and the like from the external apparatus, for example. 
     The input unit  120  is an input apparatus for receiving input of various kinds of information to the identification apparatus  100 . The input unit  120  corresponds to a keyboard, a mouse, a touch panel, or the like, for example. 
     The display unit  130  is a display apparatus for displaying various kinds of information output from the controller  160 . The display unit  130  corresponds to a liquid crystal display, a touch panel, or the like, for example. 
     The storage unit  150  has the base file  150   a , the conversion table  150   b , the codon compression file  150   c , and the codon transposition index  150   d . The storage unit  150  has the protein dictionary  150   e , the protein HMM  150   f , the dictionary index  150   g , the protein compression file  150   h , and the protein transposition index  150   i . The storage unit  150  corresponds to a semiconductor memory element such as a random access memory (RAM), a read only memory (ROM), or a flash memory or a storage such as a hard disk drive (HDD). 
     The base file  150   a  is a file holding information in which a plurality of bases are arranged. The other description of the base file  150   a  is similar to the description of the base file  150   a  described in  FIG 1 . 
     The conversion table  150   b  is a table associating a codon and a code corresponding to the codon with each other.  FIG. 6  is a diagram of an exemplary data structure of the conversion table. As illustrated in  FIG. 6 , each codon and each code are associated with each other. The code of the codon “UUU” is “40h(01000000),” for example. The letter “h” indicates that it is a hexadecimal number. 
     The codon compression file  150   c  is a file holding information in which a plurality of encoded codons are arranged. The codon compression file  150   c  is generated by the first encoding unit  160   b  described below. The other description of the codon compression file is similar to the description of the codon compression file  150   c  described in  FIG 1 . 
     The codon transposition index  150   d  is information associating the offset from the top of the codon compression file  150   c  and the codon type (the codon code) with each other.  FIG. 7  is a diagram of an exemplary data structure of the codon transposition index. In  FIG. 7 , the horizontal axis of the codon transposition index  150   d  is an axis corresponding to the offset. The vertical axis of the codon transposition index  150   d  is an axis corresponding to the codon type (the codon code). The codon transposition index  150   d  is represented by a bitmap of “0” or “1,” in which all bitmaps are set to “0” in an initial state. 
     It is assumed that the offset of the codon code at the top of the codon compression file  150   c  is “ 0 ,” for example. When a codon code “(AUG)63h” is included at the seventh position from the top of the codon compression file  150   c , the bit of a position at which the column of an offset “6” and the row of the codon code “(AUG)63h” cross each other of the codon transposition index  150   d  is “1.” 
     The protein dictionary  150   e  is information associating protein information and the codon code sequence corresponding to the protein with each other.  FIG. 8  is a diagram of an exemplary data structure of the protein dictionary. As illustrated in  FIG. 8 , this protein dictionary  150   e  associates the protein information, an amino acid code sequence, and the codon code sequence with each other. 
     The protein information includes a “code” of the protein, a “group” to which the protein belongs, and a “name” of the protein. The amino acid code sequence is a sequence of amino acid codes corresponding to the protein code (the protein type). The codon code sequence is a sequence of codon codes corresponding to the protein code (the protein type). 
     A protein “type I collagen” belongs to a group “collagen” and has a code of “8000h,” for example. An. amino acid code sequence corresponding to the code “8000h” is “02h46h59h⋅⋅⋅03h.” The codon code sequence is “02h63h78h⋅⋅⋅03h.” 
     The protein HMM  150   f  holds information on a cooccurrence rate of a protein and a protein following this protein.  FIG. 9  is a diagram of an exemplary data structure of the protein HMM. As illustrated in  FIG. 9 , this protein HMM  150   f  associates protein information and cooccurring protein information with each other. 
     The protein information includes a “code” of the protein, a “group” to which the protein belongs, and a “name” of the protein. The protein code and the cooccurrence rate are associated with the cooccurring protein information. The following describes a record on the first row of the protein HMM  150   f , for example. The probability (the cooccurrence rate) of a protein code following the protein code “8000h” being a code “8028h” is “78%.” The probability (the cooccurrence rate) of the protein code following the protein code “8000h” being a code “8132h” is “63%.” The probability (the cooccurrence rate) of the protein code following the protein code “8000h” being a code “80F5h” is “51%.” 
     The dictionary index  150   g  is information holding the offset of the break of each codon code sequence (a mass of a codon code sequence corresponding to the protein) included in the codon compression file  150   c . In the dictionary index  150   g , each break is indicated by the offset from the top of the codon compression file  150   c , for example. In the first example, the break is indicated by the offset of a top codon code of a following codon code sequence as an example. The break may be associated with the amino acid code sequence (hereinafter omitted) in addition to the codon code sequence. 
     The protein compression file  150   h  is a file holding information in which a plurality of protein codes are arranged. The protein compression file  150   h  is generated by the second encoding unit  160   d  described below. The other description of the protein compression file  150   h  is similar to the description of the protein compression file  150   h  described in  FIG 1 . 
     The protein transposition index  150   i  is information associating the offset from the top of the protein compression file  150   h  and the protein type (the protein code) with each other.  FIG 10  is a diagram of an exemplary data structure of the protein transposition index. In  FIG 10 , the horizontal axis of the protein transposition index  150   i  is an axis corresponding to the offset. The vertical axis of the protein transposition index  150   i  is an axis corresponding to the protein type (the protein code). The protein transposition index  150   i  is represented by a bitmap of “0” or “1,” in which all bitmaps are set to “0” in an initial state. 
     It is assumed that the offset of the protein code at the top of the protein compression file  150   h  is “0,” for example. When a protein code “8000h (type I collagen)” is included at the eighth position from the top of the protein compression file  150   h , the bit of a position at which the column of an offset.“7” and the row of the protein code “8000h. (type I collagen)” cross each other of the protein transposition index  150   i  is “1.” 
     The following describes  FIG. 5  again. The controller  160  has an acquisition unit  160   a , the first encoding unit  160   b , the cooccurrence totalization unit  160   c , and the second encoding unit  160   d . The controller  160  can be implemented by a central processing unit (CPU), a micro processing unit (MPU), or the like. The controller  160  can also be implemented by a hard-wired logic such as an application specific integrated circuit (ASIC) or a field programmable gate array (FPGA). 
     The acquisition unit  160   a  is a processing unit that acquires various kinds of information from a network-connected external apparatus (not illustrated) via the communication unit  110 . When having acquired the base file  150   a  from the external apparatus, for example, the acquisition unit  160   a  stores the base file  150   a  in the storage unit  150 . When the base file  150   a  is compressed. with ZIP or the like, the acquisition unit  160   a  expands the compressed base file  150   a    
     The first encoding unit  160   b  is a processing unit generating the codon compression file  150   c  based on the base file  150   a  and the conversion table  150   b . The first encoding unit  160   b  extracts bases in groups of three from the base file  150   a  and compares the extracted three bases and the conversion table  150   b  with each other to identify a code corresponding to three bases (a codon) and converts the three bases into the code. The first encoding unit  160   b  converts the codon “AUG” into a code “63h,” for example. The first encoding unit  160   b  repeatedly executes the above processing to generate the codon compression file  150   c.    
     When generating the codon compression file  150   c , the first encoding unit  160   b  generates the codon transposition index  150   d . The first encoding unit  160   h  sets “1” in a bitmap of the codon transposition index  150   d  corresponding to the converted codon code and the offset of the code of the codon compression file  150   c , for example. 
     Upon generation of the codon transposition index  150   d , the first encoding unit  160   b  may hash the codon transposition index  150   d  in order to reduce the amount of information.  FIG 11  is a diagram for illustrating exemplary processing to hash the codon transposition index. 
     The example illustrated in  FIG 11 , assuming a 32-bit register, hashes bitmaps of respective rows of the codon transposition index  150   d  based on the prime number (bottom) of “29” and “31.” The following describes a case of generating a hashed bitmap h 11  and a hashed bitmap h 12  from a bitmap b 1  as an example. 
     The bitmap b 1  indicates a bitmap as a result of extracting a certain row of a codon transposition index (e.g., the codon transposition index  150   d  illustrated in  FIG. 7 ). The hashed bitmap h 11  is a bitmap hashed by the bottom “29.” The hashed bitmap h 12  is a bitmap hashed by the bottom “31.” 
     The first encoding unit  160   b  associates the remainder of a division of each bit position of the bitmap b 1  by one bottom with the position of a hashed bitmap. When “1” is set at the corresponding bit position of the bitmap b 1 , the first encoding unit  160   b  performs processing to set “1” at the associated position of the hashed bitmap. 
     The following describes exemplary processing to generate the hashed bitmap h 11  of the bottom “29” from the bitmap b 1 . First, the first encoding unit  160   b  copies information on positions “0 to 28” of die bitmap b 1  to the hashed bitmap h 11 . Subsequently, the remainder of division of a bit position “35” of the bitmap bi by the bottom “29” is “6,” and the position “35” of the bitmap b 1  is associated with a position “6” of the hashed bitmap h 11 . “1” is set at the position “35” of the bitmap h 1 , and the first encoding unit  160   b  sets “1” at the position “6” of the hashed bitmap h 11 . 
     The remainder of division of a bit position “42” of the bitmap h 1  by the bottom “29” is “13,” and the position “42” of the bitmap h 1  is associated with a position “13” of the hashed bitmap h 11 . “1” is set at the position “42” of the bitmap bi, and the first encoding unit.  160   b  sets “1” at the position “13” of the hashed bitmap h 11 . 
     The first encoding unit  160   b  repeatedly executes the above processing for the positions of the position “29” and higher of the bitmap b 1  to generate the hashed bitmap h 11 . 
     The following describes exemplary processing to generate the hashed bitmap h 12  of the bottom “31” from the bitmap b 1 . First, the first encoding unit  160   b  copies information on positions “0 to 30” of the bitmap b 1  to the hashed bitmap h 12 . Subsequently, the remainder of division of the bit position “35” of the bitmap h 1  by the bottom “31” is “4,” and the position “35” of the bitmap b 1  is associated with a position “4” of the hashed bitmap h 12 . “1” is set at the position “35” of the bitmap b 1 , and the first encoding unit  160   b  sets “1” at the position “4” of the hashed bitmap h 12 . 
     The remainder of division of the bit position “42” of the bitmap h 1  by the bottom “31” is “11,” and the position “42” of the bitmap h 1  is associated with a position “11” of the hashed bitmap h 12 . “1” is set at the position “42” of the bitmap h 1 , and the first encoding unit  160   b  sets “1” at the position “11” of the hashed bitmap h 12 . 
     The first encoding unit  160   b  repeatedly executes the above processing for the positions of the position “31” and higher of the bitmap bi to generate the hashed bitmap h 12 . 
     The first encoding unit  160   b  performs compression by the above folding technique for each row of the codon transposition index  150   d  to hash the codon transposition index  150   d . The hashed bitmaps of the bottoms “29” and “31” are given information on the row of a bitmap as a generation source (the encoded codon type). 
     The cooccurrence totalization unit  160   c  is a processing unit generating the protein HMM  150   f  and the dictionary index  150   g  based on the codon compression file  150   c , the codon transposition index  150   d , and the protein dictionary  150   e.    
     The cooccurrence totalization unit  160   c  identifies the type and position of a protein included in the codon compression file  150   c  based on the codon transposition index  150   d . The protein is a combination of certain codons (the codon code sequence), and the codon code sequence corresponding to the protein is defined in the protein dictionary  150   e.    
       FIG 12  is a diagram for illustrating exemplary processing to identify a protein included in the codon compression file by the cooccurrence totalization unit. The following describes a case in which the position of a protein “ααα” corresponding to a codon code sequence “(UUU)40h, (UCC) 45h, (AAG)613h, (UCA)46h, (UGG)4Fh” is  identified as an example. 
     The cooccurrence totalization unit  160   c  refers to the codon transposition index  150   d  to acquire bitmaps corresponding to the respective codons “(UUU)40h, (UCC)45h, (PAG) 6Bh, (UCA) 46h, (UG)4Fh.” The bitmap of the codon code “(UUU)40h” is defined as a bitmap b_UUU. The bitmap of the codon code “(UCC)45h” is defined as a bitmap b_UCC. The bitmap of the codon code “(AAG)6Bh” is defined as a bitmap b_AAG. The bitmap of the codon code “(UCA)46h” is defined as a bitmap b_UCA. The bitmap of the codon code “(UGG)4Fh” is defined as a bitmap 
     The cooccurrence totalization unit  160   c  acquires the bitmap b_UUU and left-shifts the bitmap b_UUU to generate a bitmap b 20 . The cooccurrence totalization unit  160   c  acquires the bitmap b_UCC and performs an AND operation of the bitmap b_UCC and the bitmap b 20  to generate a bitmap b 21 . “1” is set at an offset “8” of the bitmap b 21 , which indicates that offsets 7 to 8 include the codons “(UUU)40h, (UCC)45h.” 
     The cooccurrence totalization unit  160   c  left-shifts the bitmap b 21  to generate a bitmap b 22 . The cooccurrence totalization unit  160   c  acquires the bitmap b_AAG and performs an AND operation of the bitmap b_ANG and the bitmap b 22  to generate a bitmap b 23 . “1” is set at an offset “9” of the bitmap b 23 , which indicates that offsets 7 to 9 include the codons “(UUU)40h, (UCC)45h, (AAG)6Bh.” 
     The cooccurrence totalization unit  160   c  left-shifts the bitmap b 23  to generate a bitmap b 24 . The cooccurrence totalization unit  160   c  acquires the bitmap b_UCA and performs an AND operation of the bitmap b UCA and the bitmap b 24  to generate a bitmap b 25 . “1” is set at an offset “10” of the bitmap b 25 , which indicates that offsets 7 to 10 include the codons “(UUU)40h, (UCC) 45h, (AAG)6Bh, (UCA)46h.” 
     The cooccurrence totalization unit  160   c  left-shifts the bitmap b 25  to generate a bitmap b 26 . The cooccurrence totalization unit  160   c  acquires the bitmap b_UGG and performs an AND operation of the bitmap b_UGG and the bitmap b 26  to generate a bitmap b 27 . “ 1 ” is set at an offset “11” of the bitmap b 25 , which indicates that offsets 7 to 11 include the codons “(UUU)40h, (UCC) 45h, (AAG) 6Bh, (UCA) 46h, (UGG)4Fh.” 
     By executing the processing illustrated in  FIG. 12 , the cooccurrence totalization unit  160   c  determines that the offsets “7 to 11” of the codon compression file  150   c  include the codon code sequence “(UUU)40h, (UCC) 45h, (AAG)6Bh, (UCA)46h, (UGG)4Fh” corresponding to the protein 
     The cooccurrence totalization unit  160   c  repeatedly executes the above processing for the other proteins to identify the types and the positions (offsets) of the respective proteins included in the codon compression file  150   c.    
     Subsequently, the cooccurrence totalization unit  160   c  generates the dictionary index  150   g  based on the offset of each protein included in the codon compression file  150   c  identified by the above processing. The cooccurrence totalization unit  160   c  sets the “break” of the codon code sequence corresponding to each protein included in the codon compression file  150   c  in the dictionary index  150   g . The cooccurrence totalization unit  160   c  sets a flag “1” at an offset corresponding to the break in the dictionary index  150   g , for example. In the initial value of the dictionary index  160   g , the flag corresponding to each offset is “0.” 
     In the process in which the cooccurrence totalization unit  160   c  executes the above processing, a codon code sequence from a certain offset of the codon compression file  150   c  may match a plurality of codon code sequences having different lengths included in the protein dictionary  150   e.    
     As described in.  FIG. 3 , for example, the codon code sequence from the offset P of the certain break of the codon compression file  150   c  to the offset N A  may correspond to the code of the protein A, whereas the codon code sequence from the offset P to the offset N B  may match the code of the protein B. 
     In this case, the cooccurrence totalization unit  160   c  sets the codon code of the offsets P to P+N A  as the code of the protein A and sets a flag “1” at the offset P+N A +1 in the dictionary index  150   g . The cooccurrence totalization unit  160   c  sets the codon code of the offsets P to P+N B  as the code of the protein B and sets a flag “1” at the offset P+N −   B +1 in the dictionary index  150   g . The cooccurrence totalization unit  160   c  repeatedly executes the above processing to generate the dictionary index  150   g.    
     The following describes exemplary processing to generate the protein SIMM  150   f  by the cooccurrence totalization unit  160   c . The cooccurrence totalization unit  160   c  identifies each protein code included in the codon compression file  150   c  based on the protein dictionary  150   e . The cooccurrence totalization unit  160   c  totalizer the type of a protein code following a certain protein code to calculate a cooccurrence rate with the certain protein code. 
     It is assumed that the code of the protein A has appeared M A  times in the codon compression file  150   c , for example, When the code of the protein B among various kinds of protein codes following the code of the protein A has appeared L B  times, the cooccurrence rate of the code of the protein. A and the code of the protein B is “L B /M A ×100.” The cooccurrence totalization unit  160   c  repeatedly executes the processing to calculate the cooccurrence rate for the other proteins to generate the protein HMM  150   f.    
     When the bitmap of the codon transposition index  150   d  is hashed, the cooccurrence totalization unit  160   c  reconstructs the hashed bitmap.  FIG 13  is a diagram for illustrating processing to reconstruct the hashed bitmap. The following describes a case in which the cooccurrence totalization unit  160   c  reconstructs the bitmap b 1  based on the hashed bitmap h 11  and the hashed bitmap h 12  as an example. 
     The cooccurrence totalization unit  160   c  generates an intermediate bitmap h 11 ′ from the hashed bitmap h 11  of the bottom “29.” The cooccurrence totalization unit  160   c  copies the values of positions 0 to 28 of the hashed bitmap h 11  to positions 0 to 28 of the intermediate bitmap h 11 ′, respectively. 
     The cooccurrence totalization unit  160   c  repeatedly executes processing to copy the values of the positions 0 to 28 of the hashed bitmap h 11  to the values of a position 29 and subsequent positions of the intermediate bitmap h 11 ′, respectively, every “29.” The example illustrated in  FIG 13  illustrates an example in which the values of the positions 0 to 14 of the hashed bitmap h 11  are copied to positions 29 to 43 of the intermediate bitmap h 11 ′. 
     The cooccurrence totalization unit  160   c  generates an intermediate bitmap h 12 ′ from the hashed bitmap h 12  of the bottom “31.” The cooccurrence totalization unit  160   c  copies the values of positions 0 to 30 of the hashed bitmap h 12  to positions 0 to 30 of the intermediate bitmap h 12 ′, respectively. 
     The cooccurrence totalization unit  160   c  repeatedly executes processing to copy the values of the positions 0 to 30 of the hashed bitmap h 12  to the values of a position 31 and subsequent positions of the intermediate bitmap h 12 ′, respectively, every “31.” The example illustrated in  FIG 13  illustrates an example in which the values of the positions 0 to 12 of the hashed bitmap h 12  are copied to positions 31 to 43 of the intermediate bitmap h 12 ′. 
     Upon generation of the intermediate bitmap h 11 ′ and the intermediate bitmap h 12 ′, the cooccurrence totalization unit  160   c  performs an AND operation of the intermediate bitmap h 11 ′ and the intermediate bitmap h 12 ′ to reconstruct the bitmap b 1  before hashing. The cooccurrence totalization unit  160   c  repeatedly executes similar processing for other hashed bitmaps and can thereby reconstruct each bitmap corresponding to the codon (reconstruct the codon transposition index  150   d ). 
     The following describes  FIG. 5  again. The second encoding unit  160   d  generates the protein compression file  150   h  and the protein transposition index  150   i  based on the codon compression file  150   c , the codon transposition index  150   d , the protein dictionary  150   e , the dictionary index  150   g , and the protein HMM  150   f.    
     The second encoding unit  160   d  identifies the break of the codon code sequence of each protein included in the codon compression file  150   c  based on the dictionary index  150   g . Based on the codon code sequence between each break and the protein dictionary  150   e , the second encoding unit  160   d  identifies the protein code corresponding to the codon code sequence between each break and converts the codon code sequence into the protein code. 
     When the codon code sequence following the protein code (the break) corresponds to a plurality of protein codes, the second encoding unit  160   d  identifies a protein code having the highest cooccurrence rate among the corresponding protein codes based on the protein HMM  150   f.    
     The following describes processing by the second encoding unit  160   d  when the protein code following the protein code “8000h” is “8028h” or “8132h,” for example. Referring to the protein HMM  150   f  described in.  FIG. 9 , the cooccurrence rate of the protein code “8000h” and the code “8028h” is “78%,” whereas the cooccurrence rate of the protein code “8000h” and the code “8132h” is “63%.” The cooccurrence rate of the code “8000h” and the code “8028h” is larger than the cooccurrence rate of the code “8000h” and the code “8132h,” and the second encoding unit  160   d  identifies the protein code following the protein code “8000h” as “8132h.” 
     The second encoding unit  160   d  converts the codon code sequence following the break into the identified protein code. The second encoding unit  160   d  repeatedly executes the above processing to generate the protein compression file  150   h.    
     When generating the protein compression file  150   h , the second encoding unit  160   d  generates the protein transposition index  150   i . The protein transposition index  150   i  is information associating the offset from the top of the protein compression file  150   h  and the protein code with each other. When generating the protein transposition index  150   i , the second encoding unit  160   d  may hash the bitmap of the protein transposition index  150   i . Processing to hash the bitmap of the protein transposition index  150   i  is similar to the processing to hash the bitmap of the codon transposition index  150   d  by the cooccurrence totalization unit  160   c.    
     The following describes an exemplary processing procedure by the identification apparatus  100  according to the first example.  FIG 14  is a flowchart of a processing procedure by the identification apparatus according to the first example. As illustrated in  FIG 14 , the first encoding unit  160   b  of the identification apparatus  100  compresses the base file  150   a  by codon to generate the codon compression file  150   c  and a codon transposition index  150   d  (Step S 101 ). 
     The cooccurrence totalization unit  160   c  identifies proteins included in the codon compression file  150   c  based on the protein dictionary  150   e  and the codon transposition index  150   d  (Step S 102 ). The cooccurrence totalization unit  160   c  generates the dictionary index  150   g  based on the break of each protein included in the codon compression file  150   c  (Step S 103 ). 
     The cooccurrence totalization unit  160   c  totalizes a protein included in the codon compression file  150   c  and a protein following this protein to calculate a cooccurrence. rate (Step S 104 ). The cooccurrence totalization unit  160   c  generates the protein HMM  150   f  (Step S 105 ). 
     The second encoding unit  160   d  extracts the codon code sequence corresponding to the protein from the codon compression file  150   c  based on the dictionary index  150   g  (Step S 106 ). The second encoding unit  160   d  converts the codon code sequence into the protein code based on the protein dictionary  150   e  (Step S 107 ). 
     The second encoding unit  160   d  updates the protein compression file and the protein transposition index  150   i  (Step S 108 ). If an end of the codon compression file  150   c  is reached (Yes at Step S 109 ), the second encoding unit  160   d  ends the processing. If the end of the codon compression file  150   c  is not reached (No at Step S 109 ), the second encoding unit  160   d  identifies the code (the codon code sequence) of the following protein based on the protein HMM  150   f  (Step  5110 ) and shifts the process to Step S 106 . 
     The following describes the effects of the identification apparatus  100  according to the first example. The identification apparatus  100  calculates the cooccurrence rate of a protein included in the codon compression file  150   c  and a protein following this protein to generate the protein HMM  150   f . Using the protein HMM  150   f , the identification apparatus  100  can cut out the codon code sequence of the codon compression file  150   c  in units of correct proteins. Cutting out in units of correct proteins can generate the protein compression file  150   h  with the codon compression file  150   c  encoded in units of proteins. In addition, the sequence of the proteins included in the codon compression file  150   c  can be identified, and the primary structure of the proteins including a plurality of proteins or amino acids can easily be identified. 
     Using the protein HMM  150   f , the identification apparatus  100  cuts out the codon code sequence of the codon compression file  150   c  in units of correct proteins and converts it into the code by protein to generate the protein compression file  150   h . With this operation, the base file  150   a  can be compressed in units of proteins, and a compression rate can be increased compared with the codon compression file  150   c.    
     The identification apparatus  100  generates the codon compression file  150   c  and the codon transposition index  150   d based on the base file  150   a and the conversion table  150   b . Using the codon transposition index  150   d , the arrangement of the codons included in the codon compression. file  150   c  can be identified without being expanded. 
     When generating the protein compression file  150   h , the identification apparatus  100  generates the protein transposition index  150   i . Using this protein transposition index  150   i , the arrangement of the proteins included in the protein compression file  150   h  can be identified without being expanded. 
     [b] Second Example 
       FIG 15  to  FIG 17  are diagrams for illustrating processing by an identification apparatus according to a second example. The following first describes  FIG 15 . A cooccurrence totalization unit  260   c  of the identification apparatus generates a primary structure HMM  250   b  and a primary structure dictionary index  250   c  based on the protein compression file  150   h , the protein transposition index  150   i , and a primary structure dictionary  250   a.    
     Descriptions of the protein compression file  150   h  and the protein transposition index  150   i  are similar to the descriptions of the protein compression file  150   h  and the protein transposition index  150   i  described in the first example. 
     The primary structure dictionary  250   a  is information associating a protein primary structure code and a protein code sequence with each other. In the following description, the protein primary structure will be denoted simply as a “primary structure.” The protein code sequence is information in which a plurality of protein codes are arranged. A combination of proteins (protein codes) varies in accordance with the protein primary structure, and the number of proteins corresponding to the primary structure varies. 
     The cooccurrence totalization unit  260   c  identifies a protein combination included in the protein compression file  150   h  based on the protein transposition index  150   i . The cooccurrence totalization unit  260   c  repeatedly executes processing to compare the protein combination. (the protein code sequence) and the protein code sequence of the primary structure dictionary  250   a  with each other to identify primary structure codes included in the protein compression file  150   h.    
     The cooccurrence totalization unit  260   c , in the process of repeatedly executing the above processing, sets a “break” of the protein code sequence corresponding to each primary structure included in the protein compression file  150   h  in the primary structure dictionary index  250   c.    
     In a protein code sequence “02h8028h⋅⋅03h02h80F5h⋅03h,” for example, the protein code sequence “02h8028h⋅⋅03h” is a protein code sequence corresponding to a primary structure code “F00000h.” The protein code sequence “02h80F5h⋅03h” is a protein code sequence corresponding to a primary structure code “F00001h.” In this case, the gap between the protein code sequences “02h8028h⋅⋅03h” and “02h80F5h⋅03h” is the “break.” In the primary structure dictionary index  250   c , each break is indicated by an offset from the top of the protein compression file  150   h . In the second example, the break is indicated by the offset of a top code of a following protein code sequence as an example. In the above example, the offset of the top code &lt;02h&gt; of the following “02h80F5h⋅03h” is the offset of the break. 
     In the process in which the cooccurrence totalization unit  260   c  executes the above processing, a protein code sequence from a certain offset of the protein compression file  150   h  may match a plurality of protein code sequences having different lengths included in the primary structure dictionary  250   a.    
     As illustrated in  FIG 16 , for example, a protein code sequence from an offset P of a certain break of the protein compression file  150   h  to an offset N C  may correspond to the code of a primary structure C, whereas a protein code sequence from the offset P to an offset N D  may match the code of a primary structure D. 
     In this case, the cooccurrence totalization unit  260   c  sets the protein code sequence of offsets P to P+N C  as the code of the primary structure C, sets an offset P+N C +1 as a break, and repeatedly executes the above processing. The cooccurrence totalization unit  260   c  sets the protein code sequence of offsets P to P+N D  as the code of the protein B, sets an offset P+N D +1 as a break, and repeatedly executes the above processing. 
     The cooccurrence totalization unit  260   c  totalizer an amino acid combination included in an end of the primary structure for each primary structure (the protein code sequence of each primary structure) identified by the above processing to calculate a cooccurrence rate of a certain amino acid combination and the primary structure code. It is assumed that a certain amino acid combination E has appeared M E  times in the protein compression file  150   h , for example. When the appearance times of a primary structure F among the primary structures with the amino acid combination E as their ends is L P  times, the cooccurrence. rate of the amino acid combination E and the primary structure F is “L F /M E ×100.” The cooccurrence totalization unit  260   c  repeatedly executes the processing to calculate the cooccurrence rate for each amino acid combination to generate the primary structure HMM  250   b . The primary structure HMM  250   b  is information defining the cooccurrence rate of the amino acid combination at the end of the primary structure and the primary structure. 
     The cooccurrence totalization unit  260   c  may identify the amino acid combination included in the end of the primary structure based on the relation between the protein code and the amino acid code sequence defined in the protein dictionary illustrated in  FIG. 8 . 
     The following describes  FIG 17 . An encoding unit  260   d  of the identification apparatus generates a primary structure compression file  250   d  and a primary structure transposition index  250   e  based on the protein compression file  150   h , the protein transposition index  150   i , the primary structure dictionary  250   a , the primary structure dictionary index  250   c , and the primary structure HMM  250   b . The encoding unit  260   d  is an exemplary “identification unit.” 
     The encoding unit  260   d  identifies the break of the protein code sequence of each primary structure included in the protein compression file  150   h  based on the primary structure dictionary index  250   c . Based on the protein code sequence between each break and the primary structure dictionary  250   a , the encoding unit  260   d  identifies the primary structure code corresponding to the protein code sequence with the code of each break at the top and converts the protein code sequence into the primary structure code. 
     When the protein code sequence following the primary structure code (the break) corresponds to protein code sequences of a plurality of primary structures, the encoding unit  260   d  identifies a primary structure having the highest cooccurrence rate among the corresponding primary structures based on the primary structure HMM  250   b . The encoding unit  260   d  converts the protein code sequence following the break into the identified primary structure code. The encoding unit  260   d  repeatedly executes the above processing to generate the primary structure compression file  250   d.    
     The following describes the processing by the encoding unit  260   d  with reference to  FIG 16 , for example. It is assumed that the protein code sequence with the offset P at the top corresponds to the protein code sequence corresponding to the primary structure C and the protein code sequence corresponding to the primary structure D as an example. In this case, the encoding unit  260   d  compares a cooccurrence rate CO 1  of an amino acid combination with the offset N C  of the primary structure C as an end and the primary structure C and a cooccurrence rate CO 2  of an amino acid combination with the offset N D  of the primary structure D as an end and the primary structure D with each other. 
     When the cooccurrence rate CO 1  is larger than the cooccurrence rate CO 2 , the encoding unit  260   d  identifies that the protein code sequence with the offset P at the top is the protein code sequence corresponding to the primary structure C and converts the protein code sequence of offsets P to N C  into the code of the primary structure C. The encoding unit  260   d  repeatedly executes the above processing for the protein code sequence with the offset N C  at the top. 
     On the other hand, when the cooccurrence rate CO 2  is larger than the cooccurrence rate CO 1 , the encoding unit.  260   d  identifies that the protein code sequence with the offset P at the top is the protein code sequence corresponding to the primary structure D and converts the protein code sequence of offsets P to N D  into the code of the primary structure D. The encoding unit  260   d  repeatedly executes the above processing for the protein code sequence with the offset N D  at the top. 
     When generating the primary structure compression file  250   d , the encoding unit  260   d  generates the primary structure transposition index  250   e . The primary structure transposition index  250   e  is information associating an offset from the top of the primary structure compression file  250   d  and the primary structure code with each other. 
     As described above, the identification apparatus according to the second example calculates the cooccurrence rate of a primary structure included in the protein compression file  150   h  and an amino acid combination included in the end of this primary structure to generate the primary structure HMM  250   b . Using the primary structure HMM  250   b , the identification apparatus can appropriately identify each primary structure included in the protein code sequence of the protein compression file  150   h . Each primary structure included in the protein compression file  150   h  is identified, whereby the protein compression file  150   h  can be encoded in units of primary structures. 
     The following describes an exemplary configuration of an identification apparatus  200  according to the second example.  FIG 18  is a functional block. diagram of a configuration of the identification apparatus according to the second example. As illustrated in  FIG. 18 , this identification apparatus  200  has a communication unit  210 , an input unit  220 , a display unit  230 , a storage unit  250 , and a controller  260 . 
     Descriptions of the communication unit  210 , the input unit  220 , and the display unit  230  are similar to the descriptions of the communication unit  110 , the input unit  120 , and the display unit  130  described in the first example. 
     The storage unit  250  has the base file  150   a , the conversion table  150   b , the codon compression file  150   c , and the codon transposition index  150   d . The storage unit  250  has the protein dictionary  150   e , the protein HMM  150   f , the dictionary index  150   g , the protein compression file  150   h , and the protein transposition index  150   i . The storage unit  250  has the primary structure dictionary  250   a , the primary structure HMM  250   b , the primary structure dictionary index  250   c , the primary structure compression file  250   d , and the primary structure transposition index.  250   e . The storage unit  250  corresponds to a semiconductor memory element such as a RAM, a ROM, or a flash memory or a storage such as an HDD.  
     Descriptions of the base file  150   a , the conversion table  150   b , the codon compression file  150   c , and the codon transposition index  150   d are similar to those described in the first example. Descriptions of the protein dictionary  150   e , the protein HMM  150   f , the dictionary index  150   g , the protein compression file  150   h , and the protein transposition index  150   i  are similar to those described in the first example. 
     The primary structure dictionary  250   a  is information associating the primary structure code and the protein code sequence with each other.  FIG 19  is a diagram of an exemplary data structure of the primary structure dictionary. As illustrated in  FIG 19 , this primary structure dictionary  250   a  associates primary structure information and the protein code sequence with each other. 
     The primary structure information includes a “code” of the primary structure, a “group” to which the primary structure belongs, and a “name” of the primary structure. The protein code sequence is a sequence of a protein code corresponding to the primary structure code (a primary structure type). 
     A primary structure “α primary sequence” belongs to a group “G1” and has a code of “F00000h,” for example. A protein code sequence corresponding to the code “F00000h” is “02h8028h⋅⋅⋅03h.” 
     The primary structure HMM  250   b  is information defining the cooccurrence rate of the amino acid combination at the end of the primary structure and the primary structure.  FIG. 20  is a diagram of an exemplary data structure of the primary structure HMM. As illustrated in  FIG. 20 , this primary structure HMM  250   b  associates amino acid combination information and cooccurring primary structure information with each other. 
     Each “code” corresponding to the amino acid combination and a “name” of each amino acid included in the amino acid combination are associated with the amino acid combination information. The primary structure code and the cooccurrence rate are associated with the cooccurring primary structure information. The following describes a record on the first row of the primary structure HMM  250   b , for example. The cooccurrence rate of an amino acid combination at the end “47h41h50h” and a primary structure code “F08028h” is “78%.” The cooccurrence rate of an amino acid combination at the end “47h41h50h” and a primary structure code “F08132h” is “63%.” The cooccurrence rate of an amino acid combination at the end “47h41h50h” and a primary structure code “F080F5h” is “51%.” 
     The primary structure dictionary index  250   c  is information holding the offset of the break of each protein code sequence (a mass of the protein code sequence corresponding to the primary structure) included in the protein transposition index  150   i . In the primary structure dictionary index  250   c , each break is indicated by the offset from the top of the protein compression file  150   h , for example. In the second example, the break is indicated by the offset of a top protein code of a following protein code sequence as an example. 
     The primary structure compression file  250   d  is a file holding information in which a plurality of primary structure codes are arranged. The primary structure compression file  250   d  is generated by the encoding unit  260   d  described below. The other description of the primary structure compression file  250   d  is similar to the description of the primary structure compression file  250   d  described in  FIG 17 . 
     The primary structure transposition index  250   e  is information associating the offset from the top of the primary structure compression file  250   d  and the primary structure type (the primary structure code) with each other.  FIG. 21  is a diagram of an exemplary data structure of the primary structure transposition index. In  FIG. 21 , the horizontal axis of the primary structure transposition index  250   e  is an axis corresponding to the offset. The vertical axis of the primary structure transposition index is an axis corresponding to the primary structure type (the primary structure code). The primary structure transposition index  250   e  is represented by a bitmap of “0” or “1,” in which all bitmaps are set to “0” in an initial state. 
     It is assumed that the offset of the primary structure code at the top of the primary structure compression file  250   d  is “0,” for example. When a primary structure code “F00000h (α primary sequence)” is included at the ninth position from the top of the primary structure compression file 250 d , the bit of a position at which the column of an offset “8” and the row of the primary structure code “F00000h (α primary sequence)” cross each other of the primary structure transposition index  250   e  is “1.” 
     The following describes  FIG 18  again. The controller  260  has an acquisition unit  260   a , a preprocessing unit  260   b , the cooccurrence totalization unit  260   c , and the encoding unit  260   d . The controller  260  can be implemented by a CPU, an MPU, or the like. The controller  260  can also be implemented by a hard-wired logic such as an ASIC or an FPGA. 
     The acquisition unit  260   a  is a processing unit that acquires various kinds of information from a network-connected external apparatus (not illustrated) via the communication unit  210 . When having acquired the base file  150   a  from the external apparatus, for example, the acquisition unit  260   a  stores the base file  150   a  in the storage unit  250 . When the base file  150   a  is compressed with ZIP or the like, the acquisition unit  260   a  expands the compressed base file  150   a    
     The preprocessing unit  260   b  is a processing unit corresponding to the first encoding unit  160   b , the cooccurrence totalization unit  160   c , and the second encoding unit  160   d  described in the first example. The preprocessing unit.  260   b  executes processing corresponding to the first encoding unit  160   b , the cooccurrence totalization unit  160   c , and the second encoding unit  160   d  to generate the protein compression file  150   h  and the protein transposition index  150   i.    
     The cooccurrence totalization unit  260   c  is a processing unit generating the primary structure HMM  250   b  and the primary structure dictionary index  250   c  based on the protein compression file  150   h , the protein transposition index  150   i , and the primary structure dictionary  250   a    
     The cooccurrence totalization unit  260   c  identifies the type and position of a primary structure included in the protein compression file  150   h  based on the  protein transposition index  150   i . The primary structure is a combination of certain proteins (the protein code sequence), and the protein code sequence corresponding to the primary structure is defined in the primary structure dictionary  250   a    
     The cooccurrence totalization unit  260   c  extracts the bitmap of a protein included in a certain primary structure from the protein transposition index  150   i  and repeatedly executes left-shifting and AND operation to identify the position of the certain primary structure. Descriptions of the left-shifting and the AND operation executed by the cooccurrence totalization unit  260   c  are similar to those of the cooccurrence totalization unit  160   c  described in the first example. The cooccurrence totalization unit  260   c  repeatedly executes the above processing to identify each primary structure included in the protein compression file  150   h.    
     In the process in which the cooccurrence totalization unit  260   c  executes the above processing, a protein code sequence from a certain offset of the protein compression file  150   h  may match a plurality of protein code sequences having different lengths included in the primary structure dictionary  250   a.    
     As described in  FIG 16 , for example, the protein code sequence from the offset P of the certain break of the protein compression file  150   h  to the offset N C  may correspond to the code of the primary structure C, whereas the protein code sequence from the offset P to the offset N D  may match the code of the primary structure D, for example. 
     In this case, the cooccurrence totalization unit  260   c  sets the protein code sequence of the offsets P to P+N C  as the code of the primary structure C and sets a flag “1” at the offset P+N C +1 of the primary structure dictionary index  250   c . The cooccurrence totalization unit  260   c  sets the protein code sequence of the offsets P to P+N D  as the code of the primary structure D and sets a flag “1” at the offset P+N D +1 of the primary structure dictionary index  250   c . The cooccurrence totalization unit  260   c  repeatedly executes the above processing to generate the primary structure dictionary index  250   c.    
     The following describes exemplary processing to generate the primary structure HMM  250   b  by the cooccurrence totalization unit  260   c . The cooccurrence totalization unit  260   c  identifies each primary structure code included in the protein compression file  150   h  based on the primary structure dictionary. The cooccurrence totalization unit  260   c  totalizes the amino acid combination included in the end of the primary structure for each primary structure. 
     It is assumed that the certain amino acid combination E has appeared M E  times in the protein compression file  150   h , for example. When the appearance times of the primary structure F among the primary structures with the amino acid combination E as their ends is L F  times, the cooccurrence rate of the amino acid combination E and the primary structure F is “L F /M E ×100.” The cooccurrence totalization unit  260   c  repeatedly executes the processing to calculate the cooccurrence rate for each amino acid combination to generate the primary structure. HMM  250   b . The cooccurrence totalization unit  260   c  identifies the amino acid code sequence (the amino acid combination) corresponding to the protein based on the protein dictionary  150   e.    
     The end part in which the cooccurrence totalization unit  260   c  identifies the amino acid combination is a part with a certain number of amino acids from the end toward the top. The end part may be set in advance. 
     The encoding unit  260   d  generates the primary structure compression file  250   d  and the primary structure transposition index  250   e  based on the protein compression file  150   h , the protein transposition index  150   i , the primary structure dictionary  250   a , the primary structure dictionary index  250   c , and the primary structure HMM  250   b.    
     The encoding unit  260   d  identifies the break of the protein code sequence of each primary structure included in the protein compression file  150   h  based on the primary structure dictionary index  250   c . Based on the protein code sequence between each break and the primary structure dictionary  250   a , the encoding unit  260   d  identifies the primary structure code corresponding to the protein code sequence between each break and converts the protein code sequence into the primary structure code. 
     When the protein code sequence following the primary structure code (the break) corresponds to a plurality of primary structure codes, the encoding unit  260   d  identifies a primary structure having the highest cooccurrence rate among the corresponding primary structure codes based on the primary structure HMM  250   b . The encoding unit  260   d  converts the protein code sequence following the break into the identified primary structure code. The encoding unit  260   d  repeatedly executes the above processing to generate the primary structure compression file  250   d.    
     The following describes the processing by the encoding unit  260   d  with reference to  FIG 16 , for example. It is assumed that the protein code sequence with the offset P at the top corresponds to the protein code sequence corresponding to the primary structure C and the protein code sequence corresponding to the primary structure D. In this case, the encoding unit  260   d  compares the cooccurrence rate CO 1  of the amino acid combination with the offset N C  of the primary structure C as the end and the primary structure C and the cooccurrence rate CO 2  of the amino acid combination with the offset N D  of the primary structure D as the end and the primary structure with each other. 
     When the cooccurrence rate CO 1  is larger than the cooccurrence rate CO 2 , the encoding unit  260   d  identifies that the protein code sequence with the offset P at the top is the protein code sequence corresponding to the primary structure C and converts the protein code sequence of the offsets P to N C  into the code of the primary structure C. The encoding unit  260   d  repeatedly executes the above processing for the protein code sequence with the offset N C  at the top. 
     On the other hand, when the cooccurrence rate CO 2  is larger than the cooccurrence rate CO 1 , the encoding unit  260   d  identifies that the protein code sequence with the offset P at the top is the protein code sequence corresponding to the primary structure D and converts the protein code sequence of the offsets P to N into the code of the primary structure D. The encoding unit  260   d  repeatedly executes the above processing for the protein code sequence with the offset N D  at the top. 
     When generating the primary structure compression file  250   d , the encoding unit  260   d  generates the primary structure transposition index  250   e . The primary structure transposition index  250   e  is information associating the offset from the top of the primary structure compression file  250   d  and the primary structure code with each other. 
     The following describes an exemplary processing procedure by the identification apparatus  200  according to the second example.  FIG. 22  is a flowchart of a processing procedure by the identification apparatus according to the second example. As illustrated in  FIG. 22 , the preprocessing unit  260   b  of the identification apparatus  200  executes preprocessing to generate the protein compression file  150   h  and the protein transposition index  150   i  (Step S 201 ). The preprocessing at Step S 201  corresponds to the processing described in  FIG 14  in the first example. 
     The cooccurrence totalization unit  260   c  of the identification apparatus  200  identifies primary structures included in the protein compression file  150   h  based on the primary structure dictionary  250   a  and the protein code sequences included in the protein compression file  150   h  (Step S 202 ). 
     The cooccurrence totalization unit  260   c  registers the offset of the break of each primary structure in the protein compression file  150   h  in the primary structure dictionary  250   a  (Step S 203 ). The cooccurrence totalization unit  260   c  totalizes the primary structure and the amino acid combination included in the end of the primary structure (Step S 204 ). The cooccurrence totalization unit  260   c  generates the primary structure HMM  250   b  based on a totalization result (Step S 205 ). 
     The encoding unit  260   d  of the identification apparatus  200  identifies the primary structure and the end of the primary structure (the amino acid combination) from the protein compression file  150   h  based on the primary structure dictionary index  250   c  (Step S 206 ). 
     The encoding unit  260   d  identifies a primary structure having the largest cooccurrence rate based on the primary structure HMM  250   b  (Step S 207 ). The encoding unit  260   d  updates the primary structure transposition index  250   e  (Step S 208 ). 
     When an end of the protein compression file  150   h  is reached (Yes at Step S 209 ), the encoding unit  260   d  ends the processing. On the other hand, when the end of the protein compression file  150   h  is not reached (No at Step S 209 ), the encoding unit  260   d  shifts the process to Step S 206 . 
     The following describes the effects of the identification apparatus  200  according to the second example. The identification apparatus  200  calculates the cooccurrence rate of a primary structure included in the protein compression file  150   h  and an amino acid combination included in the end of this primary structure to generate the primary structure HMM  250   b . Using the primary structure HMM  250   b , the identification apparatus  200  can appropriately identify each primary structure included in the protein code sequence of the protein compression file  150   h . Each primary structure included in the protein compression file  150   h  is identified, whereby the protein compression file  150   h  can be encoded in units of primary structures. 
     The following describes an exemplary hardware configuration of a computer implementing functions similar to those of the identification apparatus  200  ( 100 ) demonstrated in the examples.  FIG. 23  is a diagram of an exemplary hardware configuration of a computer implementing functions similar to those of the identification apparatuses according to the examples. 
     As illustrated in  FIG. 23 , this computer  300  has a CPU  301  executing various kinds of computation processing, an input apparatus  302  receiving input of data from a user, and a display  303 . The computer  300  has a reading apparatus  304  reading computer programs and the like from a storage medium and an interface apparatus  305  delivering and receiving data to and from an external apparatus or the like via a wired or wireless network. The computer  300  has a RAM  306  temporarily storing therein various kinds of information and a hard disk apparatus  307 . The apparatuses  301  to  307  are connected to a bus  308 . 
     The hard disk apparatus  307  has an acquisition computer program  307   a , a preprocessing computer program  307   b , a cooccurrence totalization computer program  307   c,  and an encoding computer program  307   d . The CPU  301  reads the acquisition computer program  307   a , the preprocessing computer program  307   b , the cooccurrence totalization computer program  307   c , and the encoding computer program  307   d  to develop them in the RAM  306 . 
     The acquisition computer program  307   a  functions as an acquisition process  306   a . The preprocessing computer program  307   b  functions as a preprocessing process  306   b . The cooccurrence totalization computer program  307   c  functions as a cooccurrence totalization process  306   c . The encoding computer program  307   d  functions as an encoding process  306   d.    
     Processing by the acquisition process  306   a  corresponds to processing by the acquisition unit  260   a . Processing by the preprocessing process  306   b  corresponds to processing by the preprocessing unit  260   b . Processing by the preprocessing unit  260   b  corresponds to processing by the first encoding unit  160   b , the cooccurrence totalization unit  160   c , and the second encoding unit  160   d . Processing by the cooccurrence totalization process  306   c  corresponds to processing by the cooccurrence totalization unit  260   c . Processing by the encoding process  306   d  corresponds to processing by the encoding unit  260   d.    
     The computer programs  307   a  to  307   d  are not necessarily needed to be stored in the hard disk apparatus  307  from the beginning. The computer programs are stored in a “portable physical medium” such as a flexible disk (FD), a compact disc read only memory (CD-ROM), a digital versatile disc (DVD), a magneto-optical disc, or an IC card to be inserted into the computer  300 , for example; the computer  300  may read and execute the computer programs  307   a  to  307   d.    
     The primary structure of proteins included in a genome can be identified. 
     All examples and conditional language recited herein are intended for pedagogical purposes of aiding the reader in understanding the invention and the concepts contributed by the inventor to further the art, and are not to be construed as limitations to such specifically recited examples and conditions, nor does the organization of such examples in the specification relate to a showing of the superiority and inferiority of the invention. Although the embodiments of the present invention have been described in detail, it should be understood that the various changes, substitutions, and alterations could be made hereto without departing from the spirit and scope of the invention.