Calculate the % similarity between 2 amino acid alignment - (Jan/08/2006 )
How to calculate the % similarity between 2 amino acid alignment sequences from BLAST searches.
What language are programming in?
Don't reinvent the wheel. Use the emboss package.
There may be no need to reinvent the wheel, which was the reason for my question. If, for example, you're using Perl, the BioPerl modules can deal with this easily.
Don't get me wrong -- I'm a big fan of EMBOSS, but what if you don't have a *nix system and don't want to use the web?
You could go for:
Although I have not tried this and I am not sure if it works...I naturally assume it does, being a biologist!
The alternative and something I would suggest every biologist has (if they are on a window$* box) is cygwin.
For those of you that don't know cygwin is a linux environment for windows. You can install all 'the good stuff' like xemacs, EMBOSS, gnuplot, grace etc and run in a linux environment (woo hoo).
Bio(perl/python/ruby/java) would indeed do the job although the later 2 are probabily overkill.
* I am a *nix fan and really don't like windows (or OS X either).