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Old 04-08-2013, 07:19 AM   #1
RamakrishnanRS
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Default Need help with BLAST Graphical Summary

Hi,

I'm pretty new to the Bioinformatics community, and I've just started working on a couple of projects. I need some help with BLAST - my scenario is:

I have created a custom BLAST Database on my HDD, and I am BLASTing a few sequences against this database. Is there any way I could create something similar to the graphical output that BLAST Web UI generates as part of its output?

Any suggestion would be welcome. Thanks!

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Old 04-08-2013, 07:28 AM   #2
westerman
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Unless things have changed in the past couple of years -- and I'll be the first to admit I do not keep up on all of the Blast changes -- you'll have to set up a WWW blast server of your own and then send your requests through a web browser. Not the most difficult thing to do but certainly a step above just running command line Blast.
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Old 04-08-2013, 07:30 AM   #3
RamakrishnanRS
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Quote:
Originally Posted by westerman View Post
Unless things have changed in the past couple of years -- and I'll be the first to admit I do not keep up on all of the Blast changes -- you'll have to set up a WWW blast server of your own and then send your requests through a web browser. Not the most difficult thing to do but certainly a step above just running command line Blast.
Thank you! I shall try that ASAP!

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Old 04-08-2013, 09:41 AM   #4
kmcarr
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In the Korf, Yandell, Bedell BLAST book they included a perl script called blast-imager.pl. It takes a BLAST tabular output report and creates a graphic of the hits aligned to the query. Here is a description from the book on Google Books.

You can download the code from the O'Reilly site (the first link above); use the "Download Example Code" link on the righthand side of the page. This tarball contains all of the code examples in the book including the blast-imager.pl script.

I have use this script a couple of times. It is certainly nothing like the output from NCBI but is kinda, sorta almost like the output you can get from locally installed www-blast. The downside of the www-blast package is that it is based on the last release of the old BLAST codebase, now officially deprecated. There is no www release for BLAST+.
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Old 04-08-2013, 09:57 AM   #5
GenoMax
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This may be another option (the graphics would not look like that on NCBI site but they can be generated or so it appears).

prfectBLAST: a platform-independent portable front end for the command terminal BLAST+ stand-alone suite

BioTechniques, Vol. 53, No. 5, November 2012, pp. 299–300

Code available here.
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