28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
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.
Miller
Webb
W
Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA. webb@bx.psu.edu
Rosenbloom
Kate
K
Hardison
Ross C
RC
Hou
Minmei
M
Taylor
James
J
Raney
Brian
B
Burhans
Richard
R
King
David C
DC
Baertsch
Robert
R
Blankenberg
Daniel
D
Kosakovsky Pond
Sergei L
SL
Nekrutenko
Anton
A
Giardine
Belinda
B
Harris
Robert S
RS
Tyekucheva
Svitlana
S
Diekhans
Mark
M
Pringle
Thomas H
TH
Murphy
William J
WJ
Lesk
Arthur
A
Weinstock
George M
GM
Lindblad-Toh
Kerstin
K
Gibbs
Richard A
RA
Lander
Eric S
ES
Siepel
Adam
A
Haussler
David
D
Kent
W James
WJ
D000818:Animals; D001483:Base Sequence; D002415:Cats; D002417:Cattle; D018387:Codon, Initiator / Q000235:genetics; D018388:Codon, Terminator / Q000235:genetics; D017124:Conserved Sequence; D030541:Databases, Genetic; D004285:Dogs; D015894:Genome, Human; D006168:Guinea Pigs; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D011817:Rabbits; D051381:Rats; D016415:Sequence Alignment / Q000379:methods*; D017384:Sequence Deletion
D018387:Codon, Initiator; D018388:Codon, Terminator