TY  - JOUR
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
Y1  - 2007/12/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1797 
EP  - 1808 
DO  - 10.1101/gr.6761107 
VL  - 17 
IS  - 12 
UR  - http://genome.cshlp.org/content/17/12/1797.abstract 
N2  - 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. 
ER  -