[Bioperl-l] SeqIO::genbank

francis@cmmt.ubc.ca francis@cmmt.ubc.ca
Wed, 12 Jul 2000 15:40:37 -0700 (PDT)

> In addition to Chris' email
> I also noticed that if you have a gb sequence file that does not have any
> features it will not read the sequence.  I'm not sure if the COMMENT and
> FEATURE tag are required by thethe Genbank spec but this doesn't seem
> to be expected behavior.  

_All_ GenBank records will have at least one FEATURE: the 'source' (all
DNA sequences come from somewhere!), e.g:

      FEATURES             Location/Qualifiers
           source          1..1042
                           /organism="Sus scrofa"
      BASE COUNT      209 a    319 c    360 g    154 t
Not all GB records have a COMMENT. All do have a BASE COUNT and
an ORIGIN though.

See ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt for more 
details on GB specs.



| B.F. Francis Ouellette                      Tel: (604) 875-3815 | 
| Director, Bioinformatics Core Facility      Fax: (425) 740-6978 | 
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