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motif_finding - 4 Finding Regulatory Motifs in DNA...

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4. Finding Regulatory Motifs in DNA Sequences (Chapter 4 and 12)
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Outline Implanting Patterns in Random Text Gene Regulation Regulatory Motifs The Motif Finding Problem Brute Force Motif Finding The Median String Problem Search Trees Branch-and-Bound Motif Search Branch-and-Bound Median String Search Consensus and Pattern Branching: Greedy Motif Search PMS: Exhaustive Motif Search
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Identifying Motifs Every gene contains a regulatory region (RR) typically stretching 100-1000 bp upstream of the transcriptional start site Genes are turned on or off by regulatory proteins These proteins bind to upstream regulatory regions of genes to either attract or block an RNA polymerase Regulatory protein transcription factor (TF) binds to a short DNA sequence called a motif or (TFBS: transcription factor binding site) So finding the same motif in multiple genes‟ regulatory regions suggests a regulatory relationship amongst those genes
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