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

• Published in: Nucleic acids research Vol. 33; no. suppl-2; pp. W262 - W266
• Main Authors: Yan, Thomas, Yoo, Danny, Berardini, Tanya Z., Mueller, Lukas A., Weems, Dan C., Weng, Shuai, Cherry, J. Michael, Rhee, Seung Y.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2005; Oxford Publishing Limited (England)
• Subjects: Arabidopsis - genetics; Arabidopsis Proteins - chemistry; Arabidopsis thaliana; DNA, Plant - chemistry; Internet; Peptides - chemistry; Sequence Analysis, DNA - methods; Sequence Analysis, Protein - methods; Software; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gki368

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.