From Bioinformatics.Org Wiki
- Biogrep - A grep that is optimized for biosequences. Biogrep is designed to locate large sets of patterns in sequence databases in parallel.
- Musca - Multiple sequence alignment of aa or nucleotide sequences / uses pattern discovery
- PatScan - PatScan is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input
- Pratt - a pattern discovery tool