# common.rb

Path: | lib/bio/db/embl/common.rb
Last Update: | Thu Nov 19 15:47:02 +0000 2009

# bio/db/embl.rb - Common methods for EMBL style database classes

Copyright: | Copyright (C) 2001-2006 Mitsuteru C. Nakao <n@bioruby.org>
License: | The Ruby License

$Id: common.rb,v 1.12.2.5 2008/05/07 12:22:10 ngoto Exp $

## Description

EMBL style databases class

This module defines a common framework among EMBL, UniProtKB, SWISS-PROT, TrEMBL. For more details, see the documentations in each embl/*.rb libraries.

EMBL style format:

        ID - identification             (begins each entry; 1 per entry)
        AC - accession number           (>=1 per entry)
        SV - sequence version           (1 per entry)
        DT - date                       (2 per entry)
        DE - description                (>=1 per entry)
        KW - keyword                    (>=1 per entry)
        OS - organism species           (>=1 per entry)
        OC - organism classification    (>=1 per entry)
        OG - organelle                  (0 or 1 per entry)
        RN - reference number           (>=1 per entry)
        RC - reference comment          (>=0 per entry)
        RP - reference positions        (>=1 per entry)
        RX - reference cross-reference  (>=0 per entry)
        RA - reference author(s)        (>=1 per entry)
        RG - reference group            (>=0 per entry)
        RT - reference title            (>=1 per entry)
        RL - reference location         (>=1 per entry)
        DR - database cross-reference   (>=0 per entry)
        FH - feature table header       (0 or 2 per entry)
        FT - feature table data         (>=0 per entry)
        CC - comments or notes          (>=0 per entry)
        XX - spacer line                (many per entry)
        SQ - sequence header            (1 per entry)
        bb - (blanks) sequence data     (>=1 per entry)
        // - termination line           (ends each entry; 1 per entry)

## Examples

     # Make a new parser class for EMBL style database entry.
     require 'bio/db/embl/common'
     module Bio
       class NEWDB < EMBLDB
         include Bio::EMBLDB::Common
       end
     end

## References

- The EMBL Nucleotide Sequence Database www.ebi.ac.uk/embl/
- The EMBL Nucleotide Sequence Database: Users Manual www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
- Swiss-Prot Protein knowledgebase. TrEMBL Computer-annotated supplement to Swiss-Prot au.expasy.org/sprot/
- UniProt uniprot.org/
- The UniProtKB/SwissProt/TrEMBL User Manual www.expasy.org/sprot/userman.html

### Required files

bio/db bio/reference bio/compat/references

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