[BioRuby] custom blast scoring matrix

[George Githinji]

Hi Martin,
Thanks for bringing the topic on list. Sometimes back i was also very
interested in custom matrices for NCBI blast.
Making custom Matrices is possible. check this out
BMC Bioinformatics 2008, 9:236 doi:10.1186/1471-2105-9-236

However making your matrices work with NCBI blast is slightly difficult as
you need to recompile the BLAST program and incoporate your modifications. I
found this a little bit not so straighforward. Lack of good documentation.

I wonder whether there is someone who has implemented the BLAST algorithm in
Ruby. (The argument is usually that the C implementation is very optimized
and good, so why would one want to implement it in ruby?) though i would not
buy that argument for learning purposes.  The closest i came to a BLAST
algorithm is an implementation of it in Perl, in the book Genomic Perl by
Rex A. Dwyer, He also outlines how to create your own matrices with code
listings in perl.

Please ping me back if you get more resources. :)
George



On Fri, Nov 20, 2009 at 8:00 PM, <bioruby-request at lists.open-bio.org> wrote:

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> Message: 1
> Date: Thu, 19 Nov 2009 15:06:22 -0500
> From: Robert Citek <robert.citek at gmail.com>
> Subject: [BioRuby] custom blast scoring matrix
> To: bioruby <bioruby at lists.open-bio.org>
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> Hello all,
>
> I would like to create a custom BLAST scoring matrix that I can use
> with NCBI's blastall.  For example, let's say I want to create a
> modified BLOSUM62 matrix called BLOSUM62ar, where the A:R score is now
> 2 instead of -1.
>
> Some questions that I have:
>
> 1) is this possible?
> 2) if it is, where can I find documentation which describes how to do this?
> 3) is the blast output different from a regular blast?
> 4) if it is different, does bio-ruby have blast parsers that can parse
> the output?
>
> Thanks in advance for any pointers and suggestions.
>
> Regards,
> - Robert
>
>
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-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/