Fine-tuning the search for microsatellites
The design and implementation is discussed of Fire?Sat2, an algorithm to detect microsatellites (short approximate tandem repeats) in DNA. The algorithm relies on deterministic finite automata. The parameters are designed to support requirements expressed by molecular biologists in data exploration. By setting the parameters of Fire?Sat2 as liberally as possible, Fire?Sat2 is able to detect more microsatellites than all other software algorithms that we have encountered. Furthermore Fire?Sat2 was found to be faster than all the other algorithms that were investigated for approximate tandem repeat detection. In addition to being fast and accurate, the Fire?Sat2 algorithm that is described is robust and easily useable.
finite automata repeat detection microsatellite detection pattern matching detection algorithm