CSE 490MT: FootPrinter

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FootPrinter (phylogenetic footprinting tool) web interface and downloadable program Presentation describing the problem and algorithms underlying FootPrinter. metK example: Phylogenetic tree input to FootPrinter Upstream DNA sequences input to FootPrinter Result produced by FootPrinter. (Look in the top frame to see the parameter settings.) Results produced by other parameter choices on this same data set: Not allowing regulatory element losses: no motifs found, even with maximum number of mutations = 4 Maximum number of mutations = 2: not bad, only one motif and a few instances of another missing Maximum number of mutations = 1: still not bad, another couple of motifs missing Motif size = 8: some motifs lost, others gained Motif size = 6: a profusion of motifs, mostly spurious Subregion change cost = 0: some new and interesting things turned up in the three Clostridia, as well as a new motif in the Lactobacillales (Streptococci, Lactococcus, etc.)

	Computer Science & Engineering University of Washington Box 352350 Seattle, WA  98195-2350 (206) 543-1695 voice, (206) 543-2969 FAX [comments to tompa]