[Bioperl-l] SearchIO, StandAloneBlastPlus

[michael watson (IAH-C)]

I think that relies on the blast database being built with the "-o T" option, which is not the default for formatdb....
________________________________________
From: bioperl-l-bounces at lists.open-bio.org [bioperl-l-bounces at lists.open-bio.org] On Behalf Of Smithies, Russell [Russell.Smithies at agresearch.co.nz]
Sent: 17 March 2010 19:48
To: 'Janine Arloth'; 'bioperl-l at lists.open-bio.org'
Subject: Re: [Bioperl-l] SearchIO, StandAloneBlastPlus

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,
Mosgiel,
New Zealand
T  +64 3 489 3809
F  +64 3 489 9174
www.agresearch.co.nz



> -----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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