[Bioperl-l] SearchIO, StandAloneBlastPlus
Russell.Smithies at agresearch.co.nz
Wed Mar 17 21:07:29 UTC 2010
Precompiled databases from NCBI are built with "-o T" but when building them yourself, the default is "-o F".
We build all ours with "-o T" as we have some extra stuff built into our to retrieve sequences for all your blast hits.
Here's an example of our sequence retrieval: https://isgcdata.agresearch.co.nz/cgi-bin/blast_results.py?filename=xCW3ez7FU46qvpKNTGNu9ZXnw&submit_time=1268859815.54&database=isgcdata_raw
> -----Original Message-----
> From: michael watson (IAH-C) [mailto:michael.watson at bbsrc.ac.uk]
> Sent: Thursday, 18 March 2010 9:48 a.m.
> To: Smithies, Russell; 'Janine Arloth'; 'bioperl-l at lists.open-bio.org'
> Subject: RE: [Bioperl-l] SearchIO, StandAloneBlastPlus
> 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,
> 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
> > hit string from the alignment with $hsp->$hit_string;)
> > Best regards
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l