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, 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.
Yan
Thomas
T
Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA.
Yoo
Danny
D
Berardini
Tanya Z
TZ
Mueller
Lukas A
LA
Weems
Dan C
DC
Weng
Shuai
S
Cherry
J Michael
JM
Rhee
Seung Y
SY
D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000737:chemistry; D018744:DNA, Plant / Q000737:chemistry; D020407:Internet; D010455:Peptides / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D029681:Arabidopsis Proteins; D018744:DNA, Plant; D010455:Peptides