Last Modified
  2013-07-17 23:07:51 +0000
Requires
  - bio/db
  - bio/reference
  - bio/compat/references

## Description

# 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