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

[Naohisa GOTO]

Hi,

There was SWlib, an implementation of Smith-Waterman algorithm for Ruby.
It was written by OKUJI K. Yoshinori in 2001.
Since it is very old, some modification would be needed for correct working.
http://bioruby.open-bio.org/contrib/swlib/

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Mon, 21 Feb 2011 12:06:07 -0500
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