[Bioperl-l] organism restricted blast search

Fernan Aguero fernan at iib.unsam.edu.ar
Thu Aug 5 09:47:20 EDT 2004

+----[ Pedro Antonio Reche <reche at research.dfci.harvard.edu> (05.Aug.2004 10:28):
| Hi, 
| I am interested in carrying out a blast (or parse a blast search) in  a 
| way that only hits from a given organism will show. This is similar to 
| what the NCBI blast site does currently I wonder if someone knows how 
| to do it using bioperl. Thanks in advance for any help. 
| Cheers 

If you use Bio::Tools:Run::RemoteBlast to run your searches
remotely at the NCBI, you can do something along the lines of:

#change a parameter
$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';

this was taken from the synopsis of the mentioned module.
You can of course replace your entrez query with whatever
you like.

If you're doing local blast searches, I guess it's not
possible. If anyone has a way of doing it, please enlighten


Fernan Aguero -  fernan at iib.unsam.edu.ar
Phone: +54 11 4580-7255/7 ext 310, Fax: +54 11 4752-9639
Check http://genoma.unsam.edu.ar/~fernan for more info.

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