Description
This track shows predictions of conserved elements produced by the phastCons
program. PhastCons is part of the
PHAST (PHylogenetic Analysis with
Space/Time models) package. The predictions are based on a phylogenetic hidden
Markov model (phylo-HMM), a type of probabilistic model that describes both
the process of DNA substitution at each site in a genome and the way this
process changes from one site to the next.
References
PhastCons
Siepel A, Bejerano G, Pedersen JS, Hinrichs A, Hou M, Rosenbloom K,
Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM,
Wilson RK, Gibbs RA, Kent WJ, Miller W, and Haussler D.
Evolutionarily conserved elements in vertebrate, insect, worm,
and yeast genomes.
Genome Res. 2005 15:1034-1050.
Chain/Net
Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D.
Evolution's cauldron: Duplication, deletion, and rearrangement
in the mouse and human genomes.
Proc Natl Acad Sci USA 2003 100(20): 11484-11489.
Multiz
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA,
Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED,
Haussler D, Miller W.
Aligning multiple genomic sequences with the threaded blockset aligner.
Genome Res. 2004 14(4):708-715.
LAST
Kielbasa SM, Wan R, Sato K, Horton P, Frith MC.
Adaptive seeds tame genomic sequence comparison.
Genome Res. 2011 Mar;21(3):487-93.