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© Oxford University Press

PATMAT: a searching and extraction program for sequence, pattern and block queries and databases

James C. Wallace and Steven Henikoff 1

Basic Sciences Division, Fred Hutchinson Cancer Research Cancer Research Center 1124 Columbia Street, Seattle, WA 98104. USA
1Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center 1124 Columbia Street, Seattle, WA 98104. USA

A program has been developed that provides molecular biologists with multiple tools for searching databases, yet uses a very simple interface. PATMATcan use protein or (translated) DNA sequences, patterns or blocks of aligned proteins as queries of databases consisting of amino acid or nucleotide sequences, patterns or blocks. The ability to search databases of blocks by ‘on-the-fly’ conversion to scoring matrices provides a new tool for detection and evaluation of distant relationships. PATMAT uses a pull-down, menu-driven interface to carry out its multiple searching, extraction and viewing functions. Each query or database type is recognized, reported, and the appropriate search carried out, with matches and alignments reported in windows as they occur. Any of the high scoring matches can be exported to a file, viewed and recalled as a query using only a few keystrokes or mouse selections. Searches of multiple database files are carried out by user selection within a window. PATMAT runs under DOS; the searching engine also runs under UNIX.

Received on August 2, 1991; accepted on December 10, 1991

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