[Bioperl-l] SeqIO::genbank

[francis@cmmt.ubc.ca]

> 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"
                           /db_xref="taxon:9823"
{..]
      BASE COUNT      209 a    319 c    360 g    154 t
      ORIGIN     
      
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.


cheers,

f.



--
| B.F. Francis Ouellette                      Tel: (604) 875-3815 | 
| Director, Bioinformatics Core Facility      Fax: (425) 740-6978 | 
| CMMT, UBC, Canada                        http://www.cmmt.ubc.ca | 
| francis@cmmt.ubc.ca                http://www.bioinformatics.ca |