[Bioperl-l] Species in a BLAST hit

Jonathan Manning bmb9jrm at bmb.leeds.ac.uk
Sun May 9 09:56:04 EDT 2004

Hi all,

Firstly apologies- I am aware this has been discussed in the archives,
but couldn't find the resolution, so was wondering if there are any
ideas (also any pointers on how to search the archives by keyword would
be useful.......!!!).

The problem is that the [organism] information seems to be truncated
from the description fields in Bio::Search::Hit::BlastHit objects, and
I'd like to be able to get the information. I've parsed the relevant
part of the 'name' string, but some of these are fairly non-sensical
(e.g. URSMA)- although if anyone has a list of what they mean that would
solve my problem as well. 

I'm aware that I could extract the information by retrieving the
relevant GenBank file, but this would slow things down significantly.

Thanks in advance,


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