28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

  1. Webb Miller1,11,
  2. Kate Rosenbloom2,
  3. Ross C. Hardison1,
  4. Minmei Hou1,
  5. James Taylor3,
  6. Brian Raney2,
  7. Richard Burhans1,
  8. David C. King1,
  9. Robert Baertsch2,
  10. Daniel Blankenberg1,
  11. Sergei L. Kosakovsky Pond4,
  12. Anton Nekrutenko1,
  13. Belinda Giardine1,
  14. Robert S. Harris1,
  15. Svitlana Tyekucheva1,
  16. Mark Diekhans2,
  17. Thomas H. Pringle5,
  18. William J. Murphy6,
  19. Arthur Lesk1,
  20. George M. Weinstock7,
  21. Kerstin Lindblad-Toh8,
  22. Richard A. Gibbs7,
  23. Eric S. Lander8,
  24. Adam Siepel9,
  25. David Haussler2,10, and
  26. W. James Kent2
  1. 1 Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA;
  2. 2 Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA;
  3. 3 Courant Institute, New York University, New York, New York 10012, USA;
  4. 4 Antiviral Research Center, University of California at San Diego, San Diego, California 92103, USA;
  5. 5 Sperling Foundation, Eugene, Oregon 97405, USA;
  6. 6 Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
  7. 7 Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
  8. 8 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;
  9. 9 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA;
  10. 10 Howard Hughes Medical Institute, Santa Cruz, California 95060, USA

Abstract

This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions.

Footnotes

  • ↵11 Corresponding author.

    ↵11 E-mail webb{at}bx.psu.edu; fax (814) 865-3176.

  • [Supplemental material is available online at www.genome.org.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6761107

    • Received June 4, 2007.
    • Accepted August 30, 2007.
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  1. Published in Advance November 5, 2007, doi: 10.1101/gr.6761107 Genome Res. 17: 1797-1808 Copyright © 2007, Cold Spring Harbor Laboratory Press

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