[Biopython] Get Organism Given Bio.Blast.Record.Blast Object

[Peter]

On Thu, Nov 5, 2009 at 12:25 AM, Matthew Strand <stran104 at chapman.edu> wrote:
> Dear users,
> Given a Bio.Blast.Record.Blast object is it possible to recover the organism
> name without using entrez to query the NCBI servers?
>
> Often the organism is listed in Bio.Blast.Record.Alignment.title but I do
> not see a way to reliably extract it from this data.

The organism is not explicitly given in BLAST results. This is
nothing to do with the Biopython parser. However, ...

The NCBI tend to encode the organism in the match title within
square brackets (and where redundant sequences have been
merged, you probably can have two organisms). You might
rely on this.

Alternatively, most (all?) of the NCBI BLAST databases will
use GI numbers, so you could use that to map to the organism.
This can be done via Entrez (online), or offline by downloading
the mapping. See:
http://lists.open-bio.org/pipermail/biopython/2009-June/005304.html

If you are using a custom BLAST database, then it all depends
on how the database was created.

Peter