791/7.36/BE490 Lecture #3 Mar.2,2004 DNA Motif Modeling 8 Discovery Chris burge
7.91 / 7.36 / BE.490 Lecture #3 Mar. 2, 2004 DNA Motif Modeling & Discovery Chris Burge
Review of DNA Seq. Comparison/Alignment Target frequencies and mismatch penalties Eukaryotic gene structure Comparative genomics applications Pipmaker(2 species comparison) Phylogenetic Shadowing(many species) Intro to DNA sequence motifs
Review of DNA Seq. Comparison/Alignment • Target frequencies and mismatch penalties • Eukaryotic gene structure • Comparative genomics applications: (2 species comparison) • Intro to DNA sequence motifs - Pipmaker - Phylogenetic Shadowing (many species)
Organization of topics Dependence Lecture Object Model Structure 5678910111 Weight 3/2 Matrix Independence G SECCAA Model 10201908060.9020.000.0ot Hidden Markov Local 3/4 Dependence Pramater Stop ass 3ss Model 3/9 Energy Model, Non-local I Covariation ModelDependence
Organization of Topics Model Dependence Lecture Object Structure Weight Matrix Model Hidden Markov Model 3/2 Independence Local 3/4 Dependence Energy Model, Covariation Model Non-local Dependence 3/9
DNA Motif Modeling Discovery Review -WMMs for splice sites Information Content of a motif The Motif Finding/Discovery Problem The Gibbs Sampler TThe gibbs Sampling Algorithm Multimedia Experience Motif Modeling -beyond Weight Matrices See Ch, 4 of Mount
DNA Motif Modeling & Discovery • Information Content of a Motif See Ch. 4 of Mount • Review - WMMs for splice sites • The Motif Finding/Discovery Problem • The Gibbs Sampler • Motif Modeling - Beyond Weight Matrices
Splicing model 5 splice site c BPX GC G G ATP branch site 7-65-4-3-2-1 ATP cacac acca ATP 3 splice site 12-11-10-98-7-65-43-2-112 cCCCccC. CCIe G
Splicing Model I branch site 5’ splice site 3’ splice site