[BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension

[Francesco Strozzi]

Hi Michael,
I have worked on a Ruby binding to the BWA fast mapping software using FFI.
With BWA you can run global alignments as well as local alignments with the
standard SW algorithm included in BWA.
This is not released as a gem yet, as it's still under testing. If you want
to check it out and see if it fits for your purpose you can find the code
here : https://github.com/fstrozzi/bioruby-bwa
The package includes two pre-compiled libraries for Mac OS X and Linux
(64bit only).

Cheers
Francesco

On Mon, Feb 21, 2011 at 18:06, Michael Barton <mail at michaelbarton.me.uk>wrote:

> Hi,
>
> Does anyone know of a ruby library for doing local and global sequence
> alignment? I'm interested in performing these kind of alignments in ruby
> but
> would prefer not to call command line tools such as EMBOSS. I think it
> could be
> useful to have a ruby gem which installs a C-extension for allowing for
> reasonably fast alignment. A cursory look on pubmed turned these links for
> C libraries.
>
> http://www.ncbi.nlm.nih.gov/pubmed/18959793
> http://www.ncbi.nlm.nih.gov/books/NBK7151/
>
> Mike
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>
>


-- 

Francesco