ANNOUNCEMENT: Pratt version 2.0 available

Inge Jonassen inge at ii.uib.no
Wed May 22 12:32:48 EST 1996


PRATT version 2.0
 
            A tool for finding flexible patterns in
                  unaligned protein sequences
 
                          Written by:
                         Inge Jonassen,
                      Dept. of Informatics,
                 University of Bergen, Norway
 
see also: http://www.ii.uib.no/~inge/Pratt.html
         http://www.ii.uib.no/~inge/Pratt2.doc.html
 
 
Pratt is a program that allows the user to efficiently search for
patterns conserved in a set of protein sequences. It allows the user
to define the class of patterns to be searched for, and then finds
conserved patterns in this class.
 
The time used by the program depends on
- the set of sequences,
- the class of patterns defined,
- the minimum number of sequences a pattern is to match,
- if an alignment or a query sequence is given, and
- the greediness of the search.
 
New in version 2.0:
 
- heuristics and branch-and-bound has been implemented speeding the
  pattern search significantly especially for sets of relatively similar
  sequences. (Using special parameters the search will be guaranteed).
 
- A multiple sequence alignment (Clustal W format) of a subset of the
  sequences can be input to Pratt, and is used to restrict the search to
  patterns consistent with the alignment
 
- A special "query" sequence (Fasta format) can be input, and Pratt will
  only search for patterns matching this. Makes it convinient to use Pratt
  together with database homology search programs.
 
- different scoring schemes for patterns (taking into account diversity
  of sequences matched and number of sequences matched)
 
Availability:
 
  The program has been implemnted in ANSI C. It has been compiled and
  run on different UNIX workstations; DEC alpha, Silicon Graphics.
  The source code is available via anonymous ftp from:
  ftp://ftp.ii.uib.no/pub/bio/Pratt/Pratt2.tar
  Documentation:
  http://www.ii.uib.no/~inge/Pratt2.doc.html
 
References:
 
  Version 1 is described in:
  "Finding flexible patterns in unaligned protein sequences" 
  Jonassen, I., Collins, J. F., Higgins, D. G.
  Protein Science (1995) 4:1587-1595.
 
  Version 2 is described in:
  "Efficient discovery of conserved patterns using a pattern graph." 
  Jonassen, I.
  Reports in Informatics no 118, March 1996, Dept. of Informatics,
  University of Bergen, Norway.
  ftp://ftp.ii.uib.no/pub/bio/papers/Pratt2_graph.ps
 
 
If you want to be informed about bug fixes, new versions etc.,
send an email to inge at ii.uib.no.
 
Inge Jonassen
-- 
                             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



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