RankMotif++ is a software designed for finding motifs whenever sequences are associated with a semi-quantitative measure of protein-DNA-binding affinity. RankMotif++ learns motif models by maximizing the likelihood of a set of binding preferences under a probabilistic model of how sequence binding affinity translates into binding preference observations.
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Xiaoyu Chen, Timothy R. Hughes & Quaid Morris (2007).
“RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors“.