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

Thomas Yan·Danny Yoo·Tanya Z Berardini·Lukas A Mueller·Dan C Weems·Shuai Weng·J Michael Cherry·Seung Y Rhee
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Abstract

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.

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ArabidopsisArabidopsis ProteinsDNA, PlantInternetPeptidesSequence Analysis, DNASequence Analysis, ProteinSoftwareUser-Computer InterfaceJournal ArticleResearch Support, U.S. Gov't, Non-P.H.S.

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Thomas Yan, Danny Yoo, Tanya Z Berardini, Lukas A Mueller, Dan C Weems, Shuai Weng, J Michael Cherry, Seung Y Rhee. 2005-07-01. PatMatch: a program for finding patterns in peptide and nucleotide sequences.. https://doi.org/10.1093/nar%2Fgki368

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