[BioSQL-l] multiple species for a sequence

Chris Fields cjfields at uiuc.edu
Sun Mar 2 01:16:24 UTC 2008


I'm looking at a bioperl bug I filed a while back that deals with  
multiple species in a sequence file, such as found for AJ428955:

ID   AJ428955; SV 1; linear; mRNA; STD; VRL; 8027 BP.
XX
AC   AJ428955;
XX
DT   09-JUL-2002 (Rel. 72, Created)
DT   15-APR-2005 (Rel. 83, Last updated, Version 4)
XX
DE   Hepatitis GB virus B subgenomic replicon neoRepB
XX
KW   core-neo fusion protein; core-neo gene; polyprotein.
XX
OS   Hepatitis GB virus B
OC   Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae.
XX
OS   Encephalomyocarditis virus
OC   Viruses; ssRNA positive-strand viruses, no DNA stage;  
Picornaviridae;
OC   Cardiovirus.

...

We could probably add support in bioperl fairly easily (Bio::Seq could  
just return an array or the first species object based on context),  
but would BioSQL support sequences like this?

chris




More information about the BioSQL-l mailing list