[Bioperl-l] SearchIO, StandAloneBlastPlus

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed Mar 17 19:48:27 UTC 2010

If you're running blast locally, use fastacmd to extract the sequences from the blast database.
Eg fastacmd -d nr -S AC147927

Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Janine Arloth
> Sent: Monday, 15 March 2010 9:16 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] SearchIO, StandAloneBlastPlus
> Hello,
> exists a possibility to get/extract the whole hit sequences? (Not only the
> hit string from the alignment with $hsp->$hit_string;)
> Best regards
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> Bioperl-l at lists.open-bio.org
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