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 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.

- DNA sequences can be analysed (complementary strand not included in analysis)
.

Availability:

  The program has been implemnted in ANSI C. It has been compiled and
  run on different UNIX workstations, DEC alpha, Sun, Silicon Graphics.
  The source code and some documentation is available via
  anonymous ftp from:
  ftp://ftp.ii.uib.no/pub/bio/Pratt/Pratt2.tar

References:

  "Finding flexible patterns in unaligned protein sequences"
  Jonassen, I., Collins, J. F., Higgins, D. G.
  Protein Science (1995) 4:1587-1595.

  "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


Installation:

- ftp Pratt.tar (for version 1) or Pratt2.tar (for version 2)
  to your local machine

- do
  $ tar xvf Pratt2.tar
  $ make

- if gcc is not installed on your system, you have to
  edit the makefile to make it use cc instead, also
  change the -O2 and -O4 options to -O

- this should give you an executable file pratt


If you want to be informed about bug fixes, new versions etc.,
send an email to inge@ii.uib.no.