HMM-applications

HMM-applications - Applications of HMMs in Computational...

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Applications of HMMs in Computational Biology BMI/CS 576 www.biostat.wisc.edu/bmi576.html Mark Craven craven@biostat.wisc.edu Fall 2011 Sequencing news this month Yersinia pestis Cannabis sativa
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The gene finding task Given: an uncharacterized DNA sequence Do: locate the genes in the sequence, including the coordinates of individual exons and introns Eukaryotic gene structure
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Sources of evidence for gene finding signals : the sequence signals (e.g. splice junctions) involved in gene expression content : statistical properties that distinguish protein- coding DNA from non-coding DNA conservation : signal and content properties that are conserved across related sequences (e.g. syntenic regions of the mouse and human genome) Gene finding: search by content encoding a protein affects the statistical properties of a DNA sequence
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Pairs of intron/exon units represent the different ways an intron can interrupt a coding sequence (after 1 st base in codon, after 2 nd base or after 3 rd base) Complementary submodel (not shown) detects genes on opposite DNA strand The GENSCAN HMM for Eukaryotic Gene Finding Figure from Burge & Karlin, Journal of Molecular Biology , 1997 Each shape denotes a functional unit of a gene or genomic region and is represented by a submodel in the HMM GENSCAN uses a variety of submodel types sequence feature model exons 5 th order inhomogenous introns, intergenic regions 5 th order homogenous poly-A, translation initiation, promoter 0 th order, fixed-length splice junctions tree-structured variable memory
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This note was uploaded on 12/15/2011 for the course BMI 576 taught by Professor Staff during the Fall '11 term at Wisc Green Bay.

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HMM-applications - Applications of HMMs in Computational...

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