6_phylohmm - Downloaded from genome.cshlp.org on Published by Cold Spring Harbor Laboratory Press Evolutionarily conserved elements in vertebrate

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10.1101/gr.3715005 Access the most recent version at doi: 2005 15: 1034-1050 Genome Res. Adam Siepel, Gill Bejerano, Jakob S. Pedersen, et al. yeast genomes Evolutionarily conserved elements in vertebrate, insect, worm, and Material Supplemental http://genome.cshlp.org/content/suppl/2005/07/18/gr.3715005.DC1.html References http://genome.cshlp.org/content/15/8/1034.full.html#related-urls Article cited in: http://genome.cshlp.org/content/15/8/1034.full.html#ref-list-1 This article cites 85 articles, 49 of which can be accessed free at: service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box at the http://genome.cshlp.org/subscriptions go to: Genome Research To subscribe to Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press on February 16, 2009 - Published by genome.cshlp.org Downloaded from
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Adam Siepel, 1,6 Gill Bejerano, 1 Jakob S. Pedersen, 1 Angie S. Hinrichs, 1 Minmei Hou, 3 Kate Rosenbloom, 1 Hiram Clawson, 1 John Spieth, 4 LaDeana W. Hillier, 4 Stephen Richards, 5 George M. Weinstock, 5 Richard K. Wilson, 4 Richard A. Gibbs, 5 W. James Kent, 1 Webb Miller, 3 and David Haussler 1,2 1 Center for Biomolecular Science and Engineering, 2 Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA; 3 Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA; 4 Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA; 5 Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu rubripes ). Parallel searches have been performed with multiple alignments of four insect species (three species of Drosophila and Anopheles gambiae ), two species of Caenorhabditis , and seven species of Saccharomyces . Conserved elements were identified with a computer program called phastCons, which is based on a two-state phylogenetic hidden Markov model (phylo-HMM). PhastCons works by fitting a phylo-HMM to the data by maximum likelihood, subject to constraints designed to calibrate the model across species groups, and then predicting conserved elements based on this model. The predicted elements cover roughly 3%–8% of the human genome (depending on the details of the calibration procedure) and substantially higher fractions of the more compact Drosophila melanogaster (37%–53%), Caenorhabditis elegans (18%–37%), and Saccharaomyces cerevisiae (47%–68%) genomes. From yeasts to vertebrates, in order of increasing genome size and general biological complexity, increasing fractions of conserved bases are found to lie outside of the exons of known protein-coding genes. In all groups, the most highly conserved elements (HCEs), by log-odds score, are hundreds or thousands of bases long. These elements share certain properties with ultraconserved
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This note was uploaded on 04/06/2010 for the course COMPUTER S COMP5647 taught by Professor Dr.ping during the Spring '10 term at York University.

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6_phylohmm - Downloaded from genome.cshlp.org on Published by Cold Spring Harbor Laboratory Press Evolutionarily conserved elements in vertebrate

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