PatMatch Notes

TAIR's PatMatch software allows you to search for short nucleotide or peptide sequences, or ambiguous/degenerate patterns. It uses the same Arabidopsis datasets as TAIR's BLAST implementation.

Features

• Set the minimum number of hits per sequence.

• Set the maximum number of hits per sequence.

• The maximum number of hits retrieved is increased to 250,000.

• The minimum number of the input pattern is 3 residues.

• Select the number of total mismatches and types of mismatches allowed.

• Improved checking of input pattern syntax.

• Modified pattern syntax for peptide searches to conform to standard one-letter codes for amino acids.

• Patterns containing regular expressions now support mismatch options.

• Patterns containing wildcards now support mismatch options.