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Phylogenomics pp 133–144Cite as

Phylogenomic Resources at the UCSC Genome Browser

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Part of the Methods in Molecular Biology™ book series (MIMB,volume 422)

Abstract

The UC Santa Cruz Genome Browser provides a number of resources that can be used for phylogenomic studies, including (1) whole-genome sequence data from a number of vertebrate species, (2) pairwise alignments of the human genome sequence to a number of other vertebrate genome, (3) a simultaneous alignment of 17 vertebrate genomes (most of them incompletely sequenced) that covers all of the human sequence, (4) several independent sets of multiple alignments covering 1% of the human genome (ENCODE regions), (5) extensive sequence annotation for interpreting those sequences and alignments, and (6) sequence, alignments, and annotations from certain other species, including an alignment of nine insect genomes. We illustrate the use of these resources in the context of assigning rare genomic changes to the branch of the phylogenetic tree where they appear to have occurred, or of looking for evidence supporting a particular possible tree topology. Sample source code for performing such studies is available.

Key Words

  • Evolutionary event
  • phylogenetic tree
  • interspersed repeat
  • chromosomal break

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Author information

Authors and Affiliations

  1. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA

    Kate Rosenbloom & Jim Kent

  2. Center for Comparative Genomics and Bioinformatics, Penn State, University Park, PA

    James Taylor & Webb Miller

  3. Department of Biology, Penn State, University Park, PA

    Stephen Schaeffer

  4. Howard Hughes Medical Institute, University of California, Santa Cruz, CA

    David Haussler

Authors
  1. Kate Rosenbloom
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  2. James Taylor
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  3. Stephen Schaeffer
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  4. Jim Kent
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  5. David Haussler
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  6. Webb Miller
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Editor information

Editors and Affiliations

  1. Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Mail Stop 4458, Texas A&M University, Raymond Stotzer Parkway, Rm 107 VMA, College Station, TX, 77843-4458, USA

    William J. Murphy PhD

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© 2008 Humana Press Inc., Totowa, NJ

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Rosenbloom, K., Taylor, J., Schaeffer, S., Kent, J., Haussler, D., Miller, W. (2008). Phylogenomic Resources at the UCSC Genome Browser. In: Murphy, W.J. (eds) Phylogenomics. Methods in Molecular Biology™, vol 422. Humana Press. https://doi.org/10.1007/978-1-59745-581-7_9

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  • DOI: https://doi.org/10.1007/978-1-59745-581-7_9

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-764-8

  • Online ISBN: 978-1-59745-581-7

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