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Nucleic Acids Research 2005 33(Web Server Issue):W262-W266; doi:10.1093/nar/gki368
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

PatMatch: a program for finding patterns in peptide and nucleotide sequences

Thomas Yan1,2, Danny Yoo1, Tanya Z. Berardini1, Lukas A. Mueller1, Dan C. Weems3, Shuai Weng4, J. Michael Cherry4 and Seung Y. Rhee1,*

1Department of Plant Biology, Carnegie Institution of Washington 260 Panama Street, Stanford, CA 94305, USA 2Department of Computer Engineering, Santa Clara University 500 El Camino Real, Santa Clara, CA 95053, USA 3National Center for Genome Resources 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA 4Department of Genetics, Stanford University Stanford, CA 94305, USA

*To whom correspondence should be addressed. Tel: +1 650 325 1521 ext 251; Fax: +1 650 325 6857; Email: rhee{at}acoma.stanford.edu

Received February 11, 2005. Revised February 28, 2005. Accepted February 28, 2005.

Here, we present PatMatch, an efficient, web-based pattern-matching program that enables searches for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences. The program can be used to find matches to a user-specified sequence pattern that can be described using ambiguous sequence codes and a powerful and flexible pattern syntax based on regular expressions. A recent upgrade has improved performance and now supports both mismatches and wildcards in a single pattern. This enhancement has been achieved by replacing the previous searching algorithm, scan_for_matches [D'Souza et al. (1997), Trends in Genetics, 13, 497–498], with nondeterministic-reverse grep (NR-grep), a general pattern matching tool that allows for approximate string matching [Navarro (2001), Software Practice and Experience, 31, 1265–1312]. We have tailored NR-grep to be used for DNA and protein searches with PatMatch. The stand-alone version of the software can be adapted for use with any sequence dataset and is available for download at The Arabidopsis Information Resource (TAIR) at ftp://ftp.arabidopsis.org/home/tair/Software/Patmatch/. The PatMatch server is available on the web at http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl for searching Arabidopsis thaliana sequences.

Present address: Lukas A. Mueller, Cornell University, Emerson Hall Room 251, Ithaca, NY 14853, USA


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