As an alternative you can use a program for finding conserved
patterns (motifs) from the unaligned sequences, for instance
Pratt (http://www.ii.uib.no/~inge/Pratt.html) - which you can
either download, compile and run on your own machine, or run
over the Web.
Dept. of Informatics, University of Bergen, HIB, N5020 BERGEN, Norway
WWW:http://www.ii.uib.no/~inge/, email:inge at ii.uib.no,
tel +47 5558 4713, fax +47 5558 4199
Robert Means wrote:
> I'm trying to find (and hopefully not have to write!) some
> software that will let me take multiple a.a. sequence alignments and then
> look for specific protein motiffs and generate statistics about the
> number of sequences containing the motiff at a certain location. Is there
> anything like this out there. It seems like some of the alignment programs
> take structure and motiffs into consideration when doing alignments.
> Anyway, if I could get some help it would be appreciated.
> Thanks in Advance,
> Robert Means
>REMEANS at husc.havard.edu>