[BioRuby] custom blast scoring matrix

[Robert Citek]

On Sat, Nov 21, 2009 at 3:58 AM, George Githinji <georgkam at gmail.com> wrote:
> 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

Thanks for the citation.  I'll have a look into that.

> 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.

That's unfortunate.  I've tried compiling NCBI blast a few times in
the past and don't ever recall having success with it, running into
the same issues you describe.  But it's been a while and maybe the
process has become easier.  I'll give it a whirl.

> 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.

Thanks.  I'll have a look at that as well.

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

Will do.

Regards,
- Robert