[BiO BB] amino acid distribution in multiple alignment

[Iddo Friedberg]

Hi Dana,

I do not know of a complete application which does that. If you are 
inclined to write around existing modules, then:

o Biopython has what you need in the Bio.Align.AlignInfo module.

o AFAIK, Bioperl do not have a calculating script of the kind you are 
looking for, but you can write something around Bio::SimpleAlign.

Hope this helped somewhat,

Iddo


Dana Reichmann wrote:
> Hi all,
> 
> I am looking for a program or script for calculation of amino acid
> distribution in specific column in ungaped multiple alignment. Most program
> I know calculates PSSM that includes weights calculation according to PAM or
> Blosum matrixes. I  just need a simple representation of amino acid
> distribution  in specific column in ungaped multiple alignment.
> 
> 
> Thanks a lot,
> Dana Reichmann

-- 
Iddo Friedberg
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171