From: "Jesús Gabriel y Galán" <jgabrielygalan@...>
Date: 2009-01-16T22:32:20+09:00
Subject: Re: Describing degerate dna strings

On Fri, Jan 16, 2009 at 7:54 AM, George George
<george.githinji@gmail.com> wrote:
> I am working with strings of 4 letter alphabet a,c,t,g that describe
> biological dna sequences. sometimes a sequence can be described as
> ac[ta]cct  meaning that at position 3 you are can have 't 'or an 'a'
> without changing the biological function of the sequence.
>
> Given ac[ta]cct as input i would like to generate a set of strings such
> that it gives me the various combination of the strings that can
> represent the above degenerate sequence e.g
>  1. actcct
>  2. acacct
>
> both satisfy the above degeneracy.
>
> any ideas?

Hi, this reminded me so much of a Ruby Quiz I solved that I wanted to
mention it :-)

http://rubyquiz.com/quiz143.html
http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-talk/274375 (my solution)

This code generates all strings that match a regexp. So we are left
with the task of converting your strings to regexps:

irb(main):010:0> require 'quiz143'
=> true
irb(main):011:0> def expand a
irb(main):012:1> re = Regexp.new(a.gsub(/\[(.*?)\]/) {|m|
"(#{$1.split(//).join("|")})"})
irb(main):013:1> re.generate
irb(main):014:1> end
=> nil
irb(main):015:0> expand "ac[ta]cct"
=> ["actcct", "acacct"]

It's probably overkill for your needs.

Jesus.