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

$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