RT Journal
A1 Miller, Webb
A1 Rosenbloom, Kate
A1 Hardison, Ross C.
A1 Hou, Minmei
A1 Taylor, James
A1 Raney, Brian
A1 Burhans, Richard
A1 King, David C.
A1 Baertsch, Robert
A1 Blankenberg, Daniel
A1 Kosakovsky Pond, Sergei L.
A1 Nekrutenko, Anton
A1 Giardine, Belinda
A1 Harris, Robert S.
A1 Tyekucheva, Svitlana
A1 Diekhans, Mark
A1 Pringle, Thomas H.
A1 Murphy, William J.
A1 Lesk, Arthur
A1 Weinstock, George M.
A1 Lindblad-Toh, Kerstin
A1 Gibbs, Richard A.
A1 Lander, Eric S.
A1 Siepel, Adam
A1 Haussler, David
A1 Kent, W. James
T1 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
JF Genome Research 
JO Genome Research 
YR 2007 
FD December 01 
VO 17 
IS 12 
SP 1797 
OP 1808 
DO 10.1101/gr.6761107 
UL http://genome.cshlp.org/content/17/12/1797.abstract 
AB 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.