PRATT version 2.0
A tool for finding flexible patterns in
unaligned protein sequences
Dept. of Informatics,
University of Bergen, Norway
see also: http://www.ii.uib.no/~inge/Pratt.htmlhttp://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)
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:
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."
Reports in Informatics no 118, March 1996, Dept. of Informatics,
University of Bergen, Norway.
If you want to be informed about bug fixes, new versions etc.,
send an email to inge at ii.uib.no.
Dept. of Informatics, University of Bergen, HIB, N5020 BERGEN, Norway
WWW:http://www.ii.uib.no/~inge/, email:inge at ii.uib.no