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Genome research DOI:10.1101/gr.6761107

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

Publication TypeJournal Article
Year of Publication2007
AuthorsMiller, W, Rosenbloom, K, Hardison, RC, Hou, M, Taylor, J, Raney, B, Burhans, R, King, DC, Baertsch, R, Blankenberg, D, 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
JournalGenome research
Date Published2007/12/01

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, downloaded in bulk by anonymous FTP from, or analyzed with the Galaxy server at 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.