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PatMatch: a program for finding patterns in peptide and nucleotide sequences
Open accessAbstract
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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Stockinger, E. J., Gilmour, S. J., & Thomashow, M. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.3.1035 · Cited by 1,807
Cited by
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Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
Metadata
- Authors
- Yan, T., Yoo, D., Berardini, T. Z., Mueller, L. A., Weems, D. C., Weng, S., Cherry, J. M., & Rhee, S. Y.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-07-01
- Volume
- 33
- Issue
- Web Server
- Pages
- W262-W266
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2139135429
- Cited by
- 185
- References
- 1
- FWCI
- 7.21
- Type
- journal article
- Language
- en
- Open access
- gold
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- Yan, T., Yoo, D., Berardini, T. Z., Mueller, L. A., Weems, D. C., Weng, S., Cherry, J. M., & Rhee, S. Y. (2005). PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Research. https://doi.org/10.1093/nar/gki368
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