[Bioperl-l] [BioSQL-l] How is is_circular recorded in BioSQL (by BioPerl)?

Hilmar Lapp hlapp at drycafe.net
Fri Aug 19 23:38:51 EDT 2011


I realize I'm chiming in here late, but the below sums it up quite well. In fact, biosequence.alphabet column was originally (pre-2002) called molecule, and the BioPerl Genbank writer defaults to alphabet() if molecule() is not defined.

-hilmar

Sent with a tap.

On Jul 25, 2011, at 9:12 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com> wrote:

> As with the is_circular hack, you could store the molecule type by adding it as an annotation in the SequenceProcessor (it's stored as $seq->molecule by BioPerl).
> 
> Actually, when round-tripping a GenBank file through BioSQL, the LOCUS line molecule type ends up in lower case, which makes me wonder if it is coming from alphabet in the biosequence table.



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