PatMatch Search for E. coli K-12 substr. MG1655PatMatch  enables you to search for short (<20 residues) nucleotide or peptide sequences, and for sequence patterns. You can search against collections of nucleotide or peptide sequences drawn from a single organism. Peptide sequences can also be drawn from a SmartTable. In addition, you can define a list of organisms in a SmartTable, and perform pattern searches against the proteomes of those organisms. PatMatch is not a replacement for BLAST. It allows for ambiguous characters, mismatches, insertions and deletions, but does not perform alignments. If you are searching sequences larger than 20 characters with no degenerate positions, please use Search > BLAST Search, which is much faster. Currently the smallest acceptable input is 3 characters and the maximum number of results is 250,000. First you will specify what set of sequences to search across, then you will specify what pattern(s) to search for.
Supported Sequence and Pattern Syntax and ExamplesThe pattern you provide is a series of characters from the following table. Some characters match only themselves in the matching sequence (e.g., AGTC), whereas other characters are wildcards that can match multiple characters in the matching sequence. For example,
 Yan, T., et al., PatMatch: a program for finding patterns in peptide and nucleotide sequences, Nucleic Acids Res. 2005.
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