PatMatch

PatMatch searches short nucleotide and peptide sequence patterns using ambiguous codes and a regular-expression-like syntax to identify cis-elements, small domains, and motifs for sequence analysis.

Key Features:

• Target sequences: Searches short nucleotide sequences (including cis-elements) and peptide sequences (including small domains and motifs).
• Pattern syntax: Uses a flexible, regular-expression-like syntax that accepts ambiguous and degenerate sequence codes.
• Mismatches and wildcards: Allows mismatches and wildcards within a single search pattern to enable approximate matches.
• Algorithm: Implements the nondeterministic-reverse grep (NR-grep) algorithm to support approximate string matching.
• Legacy comparison: NR-grep provides improved performance for complex searches compared with the previous scan_for_matches algorithm.
• Origin: Developed by The Arabidopsis Information Resource (TAIR).

Scientific Applications:

• Identification of cis-regulatory elements: Locating short nucleotide motifs corresponding to putative regulatory sequences.
• Characterization of protein motifs: Detecting small domains and motifs within peptide sequences.
• Analysis of Arabidopsis thaliana sequences: Applying pattern searches to Arabidopsis thaliana sequence datasets.

Methodology:

Pattern matching uses a regular-expression-like syntax with ambiguous/degenerate codes, supports mismatches and wildcards, and employs the nondeterministic-reverse grep (NR-grep) algorithm for approximate string matching, replacing the earlier scan_for_matches algorithm.