The exoniphy program identifies evolutionarily conserved protein-coding
exons in a multiple alignment using a phylogenetic hidden Markov
model (phylo-HMM), a statistical model that simultaneously
describes exon structure and exon evolution. This track shows exoniphy
predictions for the human Feb. 2009 (GRCh37), mouse Jul. 2007 (mm9), rat
Nov. 2004 (rn4), and dog May 2005 (canFam2) genomes, as aligned by the
multiz program. For this track, only alignments on the "syntenic
net" between human and each other species were considered.
For a description of exoniphy, see Siepel et al. (2004).
Multiz is described in Blanchette et al. (2004).
The alignment chaining methods behind the "syntenic net" are
described in Kent et al. (2003).
Thanks to Melissa Hubisz of the Siepel lab at Cornell University for
producing these predictions.
Blanchette M. et al.
Aligning multiple genomic sequences with the threaded
Genome Res. 2004;14:708-175.
Kent WJ. et al.
Evolution's cauldron: duplication, deletion, and
rearrangement in the mouse and human genomes.
P. Natl. Acad. Sci. USA. 2003;100(20):11484-11489.
Siepel A, Haussler D.
Computational identification of evolutionarily conserved
exons. RECOMB '04. 2004.