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

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, scanforₘatches 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.