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

Title28-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, Pond, SLKosakovs, 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, W Kent, J
JournalGenome Res
Volume17
Issue12
Pagination1797-808
Date Published2007 Dec
ISSN1088-9051
KeywordsAnimals, Base Sequence, Cats, Cattle, Codon, Initiator, Codon, Terminator, Conserved Sequence, Databases, Genetic, Dogs, Genome, Human, Guinea Pigs, Humans, Mice, Molecular Sequence Data, Mutagenesis, Insertional, Rabbits, Rats, Sequence Alignment, Sequence Deletion
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.

DOI10.1101/gr.6761107
Alternate JournalGenome Res.
PubMed ID17984227
PubMed Central IDPMC2099589
Grant ListR56 DK065806 / DK / NIDDK NIH HHS / United States
P41 HG002371 / HG / NHGRI NIH HHS / United States
1P41HG02371 / HG / NHGRI NIH HHS / United States
R01 DK065806 / DK / NIDDK NIH HHS / United States
DK65806 / DK / NIDDK NIH HHS / United States
N01CO12400 / CA / NCI NIH HHS / United States
N01-CO-12400 / CO / NCI NIH HHS / United States
R01 HG002238 / HG / NHGRI NIH HHS / United States
HG002238 / HG / NHGRI NIH HHS / United States