tacg - a grep for DNA

Background: Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple motifs with IUPAC degeneracies, regular expressions, patterns allowing mismatches, and probability matrices. Results: I describe a small application which allows searching for all the above pattern types individually, which further allows these atomic motifs to be assembled into logical rules for more sophisticated analysis. Conclusion: tacg is small, portable, faster and more capable than most alternatives, relatively easy to modify, and freely available in source code. Background String searching is a well-developed field of computer science, with highly optimized algorithms implemented in a variety of applications to efficiently search large collections of text [12,15]. ...

• Type: Journal
• Year: 2002
• Where: BMCBI
• Authors: Harry Mangalam
• Keywords: Algorithms, BMCBI 2002, Open Reading Frames, Pattern Matching