> On Tue, 29 Oct 1996, Wade Walke wrote:
>> > I'm looking for a program that can accept input of multiple small (10-20
> > bp long) DNA sequences (possibly hundreds of different sequences) then
> > compare and analyze them for various consensus motifs. These sequences
> > will not all fall into a single consensus motif so I cannot use a simple
> > alignment program. I what to know if any such program exists and if not
> > is there anyone willing to write such a program given the proper
> > incentive?
> >
> > Wade Walke
> > dwwalke at scripps.edu> >
The program Pratt was written to discover such conserved
patterns/motifs.
It was primarily designed for working with protein sequences, but can
also be used for analysing DNA sequences. Pratt takes as input a set of
unaligned sequences (in a single file - FastA or Swiss-Prot format), and
will discover patterns matching some minimum number of these sequences
(the user sets this minimum number). Pratt can discover PROSTIE-like
patterns including flexible gaps and ambiguous pattern positions.
See http://www.ii.uib.no/~inge/Pratt.html for more info, source
code (ANSI C) for Pratt can be downloaded from ftp.ii.uib.no
(directory /pub/bio/Pratt) or from ftp.ebi.ac.uk.
Reference:
Finding flexible patterns in unaligned protein sequences.
Inge Jonassen, John F. Collins, Desmond Higgins.
Protein Science 1995;4(8):1587-1595.
A new version of Pratt will soon be announced.
Inge.
--
Inge Jonassen,
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
