Jw, Thomas Jw, Touchman Rw, Blakesley Gg, Bouffard Sm, Beckstrom-Sternberg Eh, Margulies M, Blanchette Ac, Siepel Pj, Thomas Jc, Mcdowell
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Published in
Nature
The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a compleme...
Eh, Margulies Gm, Cooper G, Asimenos Dj, Thomas Cn, Dewey A, Siepel E, Birney D, Keefe As, Schwartz M, Hou
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Published in
Genome Research
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; com...
M, Blanchette Ed Green W, Miller David Haussler
Published in
Genome Research
It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can expect to get 98% of the bases cor...
