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

W. Miller, K. Rosenbloom, R. C. Hardison, M. Hou, J. Taylor, B. Raney, R. Burhans, D. C. King, R. Baertsch, D. Blankenberg, S. L. Kosakovsky Pond, A. Nekrutenko (+14 others)
2007 Genome Research  

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and analyzed with the Galaxy server at http://g2.bx.psu.edu. This paper 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
more » ... ly 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 (regulatory regions) or reject (coding regions and ultraconserved elements) insertions and deletions.
doi:10.1101/gr.6761107 pmid:17984227 pmcid:PMC2099589 fatcat:dbrzsps2hzcztchnbfe6ro7yia
Citation

W. Miller, K. Rosenbloom, R. C. Hardison, M. Hou, J. Taylor, B. Raney, R. Burhans, D. C. King, R. Baertsch, D. Blankenberg, S. L. Kosakovsky Pond, A. Nekrutenko, B. Giardine, R. S. Harris, S. Tyekucheva, M. Diekhans, T. H. Pringle, W. J. Murphy, A. Lesk, G. M. Weinstock, K. Lindblad-Toh, R. A. Gibbs, E. S. Lander, A. Siepel, D. Haussler, W. J. Kent. "28-Way vertebrate alignment and conservation track in the UCSC Genome Browser." Genome Research 17.12 (2007) 1797-1808