OUTLINE 149Algorithms Used and Programs Available 149Workflow and Strategies 149MEMEMAST Demo online and command Protein Motifs DNA Motifs MEME Output Algorithms 149Enumeration 149Pr ID: 125367
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OUTLINE •What are motifs? •Algorithms Used and Programs Available •Workflow and Strategies •MEME/MAST Demo (online and command Protein Motifs DNA Motifs MEME Output Algorithms •Enumeration •Probabilistic Optimization •Deterministic Optimization 1.Identify motifs2.Build a consensus Probabilistic Optimization •Uses a Gibbs sampling approach •One -merfrom each sequence is randomly picked to •Assumes most sequences will have the motif AlignAce http://atlas.med.harvard.edu/cgi-bin/alignace.pl Gibbs Motif Sampler http://bayesweb.wadsworth.org/gibbs/gibbs.html Programs Available* *incomplete listFraenkel, E., et al. Practical Strategies for Discovering Regulatory DNA Sequence Motifs PLoSComputational Biology 2:201-210 (2006) Programs Available: EMBOSS Motif Searching http://iona.wi.mit.edu/bio/tools/emboss/ •wordcount: Counts words of a specified size in a DNA •prophecy: Creates matrices/profiles from multiple •profit: Scan a sequence or database with a matrix or Programs Available: Other •Allegro (Expression) http://acgt.cs.tau.ac.il/allegro/ •CisGenome(ChIP-Seq) http://www.biostat.jhsph.edu/~hji/cisgenome MEME/MAST Demo http://meme.sdsc.edu