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

[Michael Barton]

Thank you Naohisa and Francesco for your suggestions. I will try experimenting
with these two libraries. I had also just read an interesting article on using
C extensions in Ruby which I thought might be of general interest to the
mailing list -

http://robots.thoughtbot.com/post/1037240922

On Tue, Feb 22, 2011 at 06:11:20PM +0900, Naohisa GOTO wrote:
> 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
> 
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