DNA and protein consensus search software

Inge Jonassen inge at ii.uib.no
Thu Oct 31 04:00:27 EST 1996


> 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




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