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

Webb Miller, Kate Rosenbloom, Ross Cameron Hardison, Minmei Hou, James Taylor, Brian Raney, Richard Burhans, David C. King, Robert Baertsch, Daniel James Blankenberg, Sergei L. Kosakovsky Pond, Anton Nekrutenko, Belinda Giardine, Robert Scott Harris, Svitlana Tyekucheva, Mark Diekhans, Thomas H. Pringle, William J. Murphy, Arthur Lesk, George M. WeinstockKerstin Lindblad-Toh, Richard A. Gibbs, Eric S. Lander, Adam Siepel, David Haussler, W. James Kent

Research output: Contribution to journalArticle

182 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1797-1808
Number of pages12
JournalGenome research
Volume17
Issue number12
DOIs
StatePublished - Jan 1 2007

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Vertebrates
Initiator Codon
Terminator Codon
Genome
Human Genome
Galaxies
Conserved Sequence
Nucleic Acid Regulatory Sequences
Open Reading Frames
formycin triphosphate

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Miller, W., Rosenbloom, K., Hardison, R. C., Hou, M., Taylor, J., Raney, B., ... Kent, W. J. (2007). 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome research, 17(12), 1797-1808. https://doi.org/10.1101/gr.6761107
Miller, Webb ; Rosenbloom, Kate ; Hardison, Ross Cameron ; Hou, Minmei ; Taylor, James ; Raney, Brian ; Burhans, Richard ; King, David C. ; Baertsch, Robert ; Blankenberg, Daniel James ; Kosakovsky Pond, Sergei L. ; Nekrutenko, Anton ; Giardine, Belinda ; Harris, Robert Scott ; Tyekucheva, Svitlana ; Diekhans, Mark ; Pringle, Thomas H. ; Murphy, William J. ; Lesk, Arthur ; Weinstock, George M. ; Lindblad-Toh, Kerstin ; Gibbs, Richard A. ; Lander, Eric S. ; Siepel, Adam ; Haussler, David ; Kent, W. James. / 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. In: Genome research. 2007 ; Vol. 17, No. 12. pp. 1797-1808.
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Miller, W, Rosenbloom, K, Hardison, RC, Hou, M, Taylor, J, Raney, B, Burhans, R, King, DC, Baertsch, R, Blankenberg, DJ, Kosakovsky Pond, SL, Nekrutenko, A, Giardine, B, Harris, RS, Tyekucheva, S, Diekhans, M, Pringle, TH, Murphy, WJ, Lesk, A, Weinstock, GM, Lindblad-Toh, K, Gibbs, RA, Lander, ES, Siepel, A, Haussler, D & Kent, WJ 2007, '28-Way vertebrate alignment and conservation track in the UCSC Genome Browser', Genome research, vol. 17, no. 12, pp. 1797-1808. https://doi.org/10.1101/gr.6761107

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. / Miller, Webb; Rosenbloom, Kate; Hardison, Ross Cameron; Hou, Minmei; Taylor, James; Raney, Brian; Burhans, Richard; King, David C.; Baertsch, Robert; Blankenberg, Daniel James; Kosakovsky Pond, Sergei L.; Nekrutenko, Anton; Giardine, Belinda; Harris, Robert Scott; Tyekucheva, Svitlana; Diekhans, Mark; Pringle, Thomas H.; Murphy, William J.; Lesk, Arthur; Weinstock, George M.; Lindblad-Toh, Kerstin; Gibbs, Richard A.; Lander, Eric S.; Siepel, Adam; Haussler, David; Kent, W. James.

In: Genome research, Vol. 17, No. 12, 01.01.2007, p. 1797-1808.

Research output: Contribution to journalArticle

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AU - Miller, Webb

AU - Rosenbloom, Kate

AU - Hardison, Ross Cameron

AU - Hou, Minmei

AU - Taylor, James

AU - Raney, Brian

AU - Burhans, Richard

AU - King, David C.

AU - Baertsch, Robert

AU - Blankenberg, Daniel James

AU - Kosakovsky Pond, Sergei L.

AU - Nekrutenko, Anton

AU - Giardine, Belinda

AU - Harris, Robert Scott

AU - Tyekucheva, Svitlana

AU - Diekhans, Mark

AU - Pringle, Thomas H.

AU - Murphy, William J.

AU - Lesk, Arthur

AU - Weinstock, George M.

AU - Lindblad-Toh, Kerstin

AU - Gibbs, Richard A.

AU - Lander, Eric S.

AU - Siepel, Adam

AU - Haussler, David

AU - Kent, W. James

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