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

[Raoul Bonnal]

Hi Michael,
thanks for the post.
Why not open a Geek section on the wiki for this type of links ?
  _____  

From: Michael Barton [mailto:mail at michaelbarton.me.uk]
To: BioRuby Mailing List [mailto:bioruby at lists.open-bio.org]
Sent: Tue, 22 Feb 2011 17:48:21 +0100
Subject: Re: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh C-extension

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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