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

Miller, W., Rosenbloom, K., Hardison, R. C., Hou, M., Taylor, J., Raney, B., Burhans, R., King, D. C., Baertsch, R., Blankenberg, D., Kosakovsky Pond, S. L., Nekrutenko, A., Giardine, B., Harris, R. S., Tyekucheva, S., Diekhans, M., Pringle, T. H., Murphy, W. J., Lesk, A., Weinstock, G. M., Lindblad-Toh, K., Gibbs, R. A., Lander, E. S., Siepel, A., Haussler, D., Kent, W. J. (2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research, 17 (12). pp. 1797-808. ISSN 1088-9051

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URL: http://www.ncbi.nlm.nih.gov/pubmed/17984227
DOI: 10.1101/gr.6761107

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.

Item Type: Paper
Uncontrolled Keywords: Animals Base Sequence Cats Cattle Codon, Initiator/genetics Codon, Terminator/genetics *Conserved Sequence *Databases, Genetic Dogs Genome, Human Guinea Pigs Humans Mice Molecular Sequence Data Mutagenesis, Insertional Rabbits Rats Sequence Alignment/*methods Sequence Deletion
Subjects: bioinformatics
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > alignment > sequence alignment
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 14 Jan 2015 16:31
Last Modified: 14 Jan 2015 16:31
PMCID: PMC2099589
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31083

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