[Bioperl-l] SearchIO, StandAloneBlastPlus

[Smithies, Russell]

It's all a bit complicated as this page is on a public site but our blast server is internal and restricted so there's no direct communication between them.
The public site takes the data from the blast requect and writes it to a template file then puts it in a folder that the internal blast server checks every 10 seconds. When a new request is found, it does the blast , creates the image and map with Bio::Graphics, then transfers it to a folder on the public server. As a sneaky bodge so I don't have to transfer the image, it's base64 encoded in the html then stripped out later. The blast result page keeps refreshing until it sees the required result has returned then displays the page.
It sounds a bit odd but as blast runs on one of our main servers, we don't want anyone to be able to "accidently" run commands on it - no one has hacked our servers yet :)

There's some good stuff in the BioPerl howtos http://www.bioperl.org/wiki/HOWTO:Graphics and http://www.bioperl.org/wiki/HOWTO:SearchIO
Bio::SearchIO::Writer::HTMLResultWriter can be quite useful though ours is html-ized 'manually' as it's streamed through a post-processing script.

--Russell

From: Janine Arloth [mailto:janine.arloth at googlemail.com]
Sent: Thursday, 18 March 2010 10:33 a.m.
To: Smithies, Russell
Subject: Re: [Bioperl-l] SearchIO, StandAloneBlastPlus

Thank you very much.
Can I ask you, how you get the figure in the blast output (blastmap)? I use use Bio::Graphics;
But i did not see how to create this figure?

Best Regards

Am 17.03.2010 um 22:07 schrieb Smithies, Russell:


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


--Russell



-----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<mailto:'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<mailto: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<mailto:'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<mailto: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<http://www.agresearch.co.nz>



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org<mailto: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<mailto: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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