BioOptimizer is an algorithm designed to clean up Motif-finding output by finding the configuration of motif start sites that maximizes a scoring function based on the log-posterior distribution given in Jensen et al (200X). In addition, the algorithm allows the motif width to vary and attempts to find the best motif width, again in terms of maximizing the scoring function.
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Shane T. Jensen and Jun S. Liu
BioOptimizer: a Bayesian scoring function approach to motif discovery.
Bioinformatics. 2004 Jul 10;20(10):1557-64. Epub 2004 Feb 12.