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

Thomas Yan1, Danny Yoo, Tanya Z Berardini

  • 1Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA.

Nucleic Acids Research
|June 28, 2005
PubMed
Summary

PatMatch is an upgraded web tool for finding short DNA or peptide sequences using flexible patterns. It now efficiently handles mismatches and wildcards, improving sequence analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate identification of short nucleotide and peptide sequences is crucial for understanding biological functions.
  • Existing pattern-matching tools may have limitations in handling complex sequence patterns, mismatches, and wildcards simultaneously.

Purpose of the Study:

  • To present PatMatch, an enhanced web-based program for efficient pattern matching of nucleotide and peptide sequences.
  • To improve the performance and flexibility of sequence pattern searching, including approximate matching.

Main Methods:

  • Developed PatMatch, a web-based pattern-matching program utilizing regular expressions for flexible pattern definition.
  • Replaced the previous searching algorithm with nondeterministic-reverse grep (NR-grep) to support mismatches and wildcards.

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  • Tailored NR-grep for DNA and protein sequence searches, enhancing approximate string matching capabilities.

    • Main Results:

    • PatMatch efficiently searches for short nucleotide (e.g., cis-elements) and peptide (e.g., motifs) sequences.
    • The upgraded program supports user-specified patterns with ambiguous codes, mismatches, and wildcards in a single search.
    • NR-grep integration significantly improved performance for approximate sequence matching.

    Conclusions:

    • PatMatch provides an efficient and versatile tool for sequence pattern analysis in bioinformatics.
    • The enhanced capabilities of PatMatch facilitate deeper insights into sequence function and structure.
    • Both a downloadable stand-alone version and a web server are available for broad accessibility.