10.1 GenBank Files

The primary repositories for genetic information are the NCBI GenBank, EMBL in Europe, and the DNA Data Bank of Japan (DDBJ). All have almost identical information due to international cooperative agreements. Each entry or record in GenBank or its mirror sites may contain identifying, descriptive, and genetic information in ASCII-format files. Each record is written in a specific standard format, organized so that both humans and computer programs can extract the desired information with reasonable ease.

Let's look at a relatively short GenBank record and at how the fields are defined, before writing any code. I'll save this information in a file called record.gb, for use in later programs.

LOCUS       AB031069     2487 bp    mRNA            PRI       27-MAY-2000
DEFINITION  Homo sapiens PCCX1 mRNA for protein containing CXXC domain 1,
            complete cds.
ACCESSION   AB031069
VERSION     AB031069.1  GI:8100074
KEYWORDS    .
SOURCE      Homo sapiens embryo male lung fibroblast cell_line:HuS-L12 cDNA to
            mRNA.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (sites)
  AUTHORS   Fujino,T., Hasegawa,M., Shibata,S., Kishimoto,T., Imai,Si. and
            Takano,T.
  TITLE     PCCX1, a novel DNA-binding protein with PHD finger and CXXC domain,
            is regulated by proteolysis
  JOURNAL   Biochem. Biophys. Res. Commun. 271 (2), 305-310 (2000)
  MEDLINE   20261256
REFERENCE   2  (bases 1 to 2487)
  AUTHORS   Fujino,T., Hasegawa,M., Shibata,S., Kishimoto,T., Imai,S. and
            Takano,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-AUG-1999) to the DDBJ/EMBL/GenBank databases.
            Tadahiro Fujino, Keio University School of Medicine, Department of
            Microbiology; Shinanomachi 35, Shinjuku-ku, Tokyo 160-8582, Japan
            (E-mail:fujino@microb.med.keio.ac.jp,
            Tel:+81-3-3353-1211(ex.62692), Fax:+81-3-5360-1508)
FEATURES             Location/Qualifiers
     source          1..2487
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /sex="male"
                     /cell_line="HuS-L12"
                     /cell_type="lung fibroblast"
                     /dev_stage="embryo"
     gene            229..2199
                     /gene="PCCX1"
     CDS             229..2199
                     /gene="PCCX1"
                     /note="a nuclear protein carrying a PHD finger and a CXXC
                     domain"
                     /codon_start=1
                     /product="protein containing CXXC domain 1"
                     /protein_id="BAA96307.1"
                     /db_xref="GI:8100075"
                     /translation="MEGDGSDPEPPDAGEDSKSENGENAPIYCICRKPDINCFMIGCD
                     NCNEWFHGDCIRITEKMAKAIREWYCRECREKDPKLEIRYRHKKSRERDGNERDSSEP
                     RDEGGGRKRPVPDPDLQRRAGSGTGVGAMLARGSASPHKSSPQPLVATPSQHHQQQQQ
                     QIKRSARMCGECEACRRTEDCGHCDFCRDMKKFGGPNKIRQKCRLRQCQLRARESYKY
                     FPSSLSPVTPSESLPRPRRPLPTQQQPQPSQKLGRIREDEGAVASSTVKEPPEATATP
                     EPLSDEDLPLDPDLYQDFCAGAFDDHGLPWMSDTEESPFLDPALRKRAVKVKHVKRRE
                     KKSEKKKEERYKRHRQKQKHKDKWKHPERADAKDPASLPQCLGPGCVRPAQPSSKYCS
                     DDCGMKLAANRIYEILPQRIQQWQQSPCIAEEHGKKLLERIRREQQSARTRLQEMERR
                     FHELEAIILRAKQQAVREDEESNEGDSDDTDLQIFCVSCGHPINPRVALRHMERCYAK
                     YESQTSFGSMYPTRIEGATRLFCDVYNPQSKTYCKRLQVLCPEHSRDPKVPADEVCGC
                     PLVRDVFELTGDFCRLPKRQCNRHYCWEKLRRAEVDLERVRVWYKLDELFEQERNVRT
                     AMTNRAGLLALMLHQTIQHDPLTTDLRSSADR"
BASE COUNT      564 a    715 c    768 g    440 t
ORIGIN      
        1 agatggcggc gctgaggggt cttgggggct ctaggccggc cacctactgg tttgcagcgg
       61 agacgacgca tggggcctgc gcaataggag tacgctgcct gggaggcgtg actagaagcg
      121 gaagtagttg tgggcgcctt tgcaaccgcc tgggacgccg ccgagtggtc tgtgcaggtt
      181 cgcgggtcgc tggcgggggt cgtgagggag tgcgccggga gcggagatat ggagggagat
      241 ggttcagacc cagagcctcc agatgccggg gaggacagca agtccgagaa tggggagaat
      301 gcgcccatct actgcatctg ccgcaaaccg gacatcaact gcttcatgat cgggtgtgac
      361 aactgcaatg agtggttcca tggggactgc atccggatca ctgagaagat ggccaaggcc
      421 atccgggagt ggtactgtcg ggagtgcaga gagaaagacc ccaagctaga gattcgctat
      481 cggcacaaga agtcacggga gcgggatggc aatgagcggg acagcagtga gccccgggat
      541 gagggtggag ggcgcaagag gcctgtccct gatccagacc tgcagcgccg ggcagggtca
      601 gggacagggg ttggggccat gcttgctcgg ggctctgctt cgccccacaa atcctctccg
      661 cagcccttgg tggccacacc cagccagcat caccagcagc agcagcagca gatcaaacgg
      721 tcagcccgca tgtgtggtga gtgtgaggca tgtcggcgca ctgaggactg tggtcactgt
      781 gatttctgtc gggacatgaa gaagttcggg ggccccaaca agatccggca gaagtgccgg
      841 ctgcgccagt gccagctgcg ggcccgggaa tcgtacaagt acttcccttc ctcgctctca
      901 ccagtgacgc cctcagagtc cctgccaagg ccccgccggc cactgcccac ccaacagcag
      961 ccacagccat cacagaagtt agggcgcatc cgtgaagatg agggggcagt ggcgtcatca
     1021 acagtcaagg agcctcctga ggctacagcc acacctgagc cactctcaga tgaggaccta
     1081 cctctggatc ctgacctgta tcaggacttc tgtgcagggg cctttgatga ccatggcctg
     1141 ccctggatga gcgacacaga agagtcccca ttcctggacc ccgcgctgcg gaagagggca
     1201 gtgaaagtga agcatgtgaa gcgtcgggag aagaagtctg agaagaagaa ggaggagcga
     1261 tacaagcggc atcggcagaa gcagaagcac aaggataaat ggaaacaccc agagagggct
     1321 gatgccaagg accctgcgtc actgccccag tgcctggggc ccggctgtgt gcgccccgcc
     1381 cagcccagct ccaagtattg ctcagatgac tgtggcatga agctggcagc caaccgcatc
     1441 tacgagatcc tcccccagcg catccagcag tggcagcaga gcccttgcat tgctgaagag
     1501 cacggcaaga agctgctcga acgcattcgc cgagagcagc agagtgcccg cactcgcctt
     1561 caggaaatgg aacgccgatt ccatgagctt gaggccatca ttctacgtgc caagcagcag
     1621 gctgtgcgcg aggatgagga gagcaacgag ggtgacagtg atgacacaga cctgcagatc
     1681 ttctgtgttt cctgtgggca ccccatcaac ccacgtgttg ccttgcgcca catggagcgc
     1741 tgctacgcca agtatgagag ccagacgtcc tttgggtcca tgtaccccac acgcattgaa
     1801 ggggccacac gactcttctg tgatgtgtat aatcctcaga gcaaaacata ctgtaagcgg
     1861 ctccaggtgc tgtgccccga gcactcacgg gaccccaaag tgccagctga cgaggtatgc
     1921 gggtgccccc ttgtacgtga tgtctttgag ctcacgggtg acttctgccg cctgcccaag
     1981 cgccagtgca atcgccatta ctgctgggag aagctgcggc gtgcggaagt ggacttggag
     2041 cgcgtgcgtg tgtggtacaa gctggacgag ctgtttgagc aggagcgcaa tgtgcgcaca
     2101 gccatgacaa accgcgcggg attgctggcc ctgatgctgc accagacgat ccagcacgat
     2161 cccctcacta ccgacctgcg ctccagtgcc gaccgctgag cctcctggcc cggacccctt
     2221 acaccctgca ttccagatgg gggagccgcc cggtgcccgt gtgtccgttc ctccactcat
     2281 ctgtttctcc ggttctccct gtgcccatcc accggttgac cgcccatctg cctttatcag
     2341 agggactgtc cccgtcgaca tgttcagtgc ctggtggggc tgcggagtcc actcatcctt
     2401 gcctcctctc cctgggtttt gttaataaaa ttttgaagaa accaaaaaaa aaaaaaaaaa
     2461 aaaaaaaaaa aaaaaaaaaa aaaaaaa
//

Even if you're used to seeing GenBank files, it's worth taking the time to look one over, while considering how you would write a program to extract various parts of the data. For instance, how would you extract the sequence data? What's the format of the FEATURES table and its various subfields?

There's a lot of information packed into a typical GenBank entry, and it's important to be able to separate the different parts. For instance, if you can extract the sequence, you can search for motifs, calculate statistics on the sequence, look for similarity with other sequences, and so forth. Similarly, you'll want to separate out—or parse—the various parts of the data annotation. In GenBank, this includes ID numbers, gene names, genus and species, publications, etc. The FEATURES table part of the annotation can include specific information about the DNA, such as the locations of exons, regulatory regions, important mutations, and so on.

The format specification of GenBank files and a great deal of other information about GenBank can be found in the GenBank release notes, gbrel.txt, on the GenBank web site at ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt.

gbrel.txt gives complete detail about the structure of GenBank files to help programmers, so you may want to refer to it as your searches become more complex. As a Perl programmer, you won't need all of the detail because you can parse data using regular expressions or the split function. You need to get the data out and make it available to your programs. The code that accomplishes this task can be fairly simple, as you will see in this chapter.