GenericBioMatch: A novel generic pattern match algorithm for biological sequences

GenericBioMatch is a novel algorithm for exact match in biological sequences. It allows the sequence motif pattern to contain one or more wild card letters (eg. Y, R, W in DNA sequences) and one or more gaps of any number of bases. GenericBioMatch is a relatively fast algorithm as compared to probabilistic algorithms, and has very little computational overhead. It is able to perform exact match of protein motifs as well as DNA motifs. This algorithm can serve as a quick validation tool for implementation of other algorithms, and can also serve as a supporting tool for probabilistic algorithms in order to reduce computational overhead. This algorithm has been implemented in the BioMiner software (http://iit-iti.nrc-cnrc.gc.ca/biomine e.trx), a suite of Java tools for integrated data mining in genomics. It has been tested successfully with DNA sequences from human, yeast, and Arabidopsis.