Fine-tuning the search for microsatellites

The design and implementation is discussed of FireμSat2, 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 FireμSat2 as liberally as possible, FireμSat2 is able to detect more microsatellites than all other software algorithms that we have encountered. Furthermore FireμSat2 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 FireμSat2 algorithm that is described is robust and easily useable.