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Pratt 2.1, a tool for finding flexible patterns in unaligned protein sequences
Introduction
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.
The Pratt program has been written by Inge Jonassen, BioInformatics Group, Department of Informatics, University of Bergern (Norway). A WWW interface to Prat is also available.
New features in version 2.1
When showing the sequence segments matching each pattern, the sequence symbols matching non-wildcard positions (components) in the pattern, are written in upper-case while sequence symbols matching wild-cards are in lower-case. Also, gaps (-) are added to align the symbols matching each pattern component.
Summary information about where the patterns match in the sequences is written horizontally or vertically.
The user can restrict where in the sequences patterns should be looked for. This can be useful for example if the user knows some constraints on the position of the patterns in one or more of the sequences.
A few bugs in version 2.0 have been fixed in 2.1.
Command line search control -- the user can now choose values for all parameters that are in the menu directly from the command line. This makes it quicker for experienced user to specify his/her search, and also makes it easier to call Pratt from inside other programs.
The menu has been changed - two-letter commands are used.
When using Pratt interactively (using the menu), some summary information about the search parameters will be shown after the user asks the search to be started, and the user is given the opportunity to go back to the menu to change parameter values.
On-line help is available from the menu by typing "help <option>" where option is one of the options in the menu or help for general help about Pratt.
Availability:
The program has been implemnted in ANSI C. It has been compiled and run on different UNIX workstations, DEC alpha, Sun, Silicon Graphics, and also on Linux PC's (Pentium and DEC alpha).
Announced by: Inge Jonassen
Resources and further information:
Department of Informatics -- University of Bergen (Norway)
http://www.ii.uib.no/index_e.html
Pratt homepage
http://www.ii.uib.no/~inge/Pratt.html
Pratt source code
ftp.ii.uib.no/pub/bio/Pratt/Pratt2.1.tar
Contact: Inge Jonassen, e-mail: inge@ii.uib.no
Literature:
- "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. Submitted to CABIOS.
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