Alignment programms?

Mr. G. Morley gmorley at crc.ac.uk
Tue Jul 12 10:39:26 EST 1994

 hello all..
            I hope somepne will be able to help me with this one.
I have about 100 short amino acid fragments (6 amino acids each)
that I want to sort and characterise depending on their homology to each
  What I am really looking for is a programm in either unix or ms-dos
that will compare each one and sort them into groups.
 The kibd of programme I had in mind is similar to what XDAP/XBAP
does for DNA sequences..ie: if sequences do not match one already
present in a newly formed contig it generates a new contig and places
it in there.
 I have tried Cluster at the HGMP..but unfortuantely like Pileup
it attempts to align sequences even if they have no Identitise/homologies
if it has been asked to look at them..I am really looking for a 
programme which will refuse to align proteins if they do not have
a certain homology value.
 If anyone has any suggestions/ideas or has noticed that I have failed
to exploit one of the programms I have mentioned above I would
be eternaly gratefull.
 If a programme  is recomended I would also appreciate an ftp site
that I can download it from.
 Thanks in advance,
                  Gary Morley

                        gmorley at rpms.ac.uk

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