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
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.

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 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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