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Finding Regulatory Motifs in DNA Sequences - UCSD CSE

Introduction to Bioinformatics AlgorithmsFinding Regulatory Motifs in DNA Sequences An Introduction to Bioinformatics Implanting Patterns in Random Text Gene Regulation Regulatory Motifs The Gold Bug Problem 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 An Introduction to Bioinformatics Sampleatgaccgggatactgataccgtatttggcctagg cgtacacattagataaacgtatgaagtacgttagactcgg cgccgccgacccctattttttgagcagatttagtgacctg gaaaaaaaatttgagtacaaaacttttccgaatactgggc ataaggtacatgagtatccctgggatgacttttgggaaca ctatagtgctctcccgatttttgaatatgtaggatcattc gccagggtccgagctgagaattggatgaccttgtaagtgt tttccacgcaatcgcgaaccaacgcggacccaaaggcaag accgataaaggagatcccttttgcggtaatgtgccgggag gctggttacgtagggaagccctaacggacttaatggccca cttagtccacttataggtcaatcatgttcttgtgaatgga tttttaactgagggcatagaccgcttggcgcacccaaatt cagtgtgggcga

Finding Regulatory Motifs in ... • Nucleotides in motifs encode for a message in the “genetic” language. Symbols in “The Gold Bug” encode for a message in English • In order to solve the problem, we analyze the frequencies of patterns in DNA/Gold Bug message.

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