MaxFlow, a greedy algorithm, using a novel consistency score to estimate the relative likelihood of alternative paths of transitive alignment. In contrast to traditional profile models of amino acid preferences, MaxFlow models the probability that two positions are structurally equivalent and retains high information content across large distances in sequence space. Thus, MaxFlow is able to identify sparse and narrow active-site sequence signatures which are embedded in high-entropy sequence segments in the structure based multiple alignment of large diverse enzyme superfamilies.
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J Comput Biol. 2004;11(5):843-57.
Accurate detection of very sparse sequence motifs.
Heger A, Lappe M, Holm L.