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 Mar. 2006 (hg18), mouse Feb. 2006 (mm8), 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.
The predictions for mouse Feb. 2006 (mm8) were lifted to
the mouse Jul. 2007 (mm9) genome.
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 Brona Brejova of Cornell University for producing these predictions.
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,
Baertsch R, Rosenbloom K, Clawson H, Green ED, et al.
Aligning multiple genomic sequences with the threaded blockset aligner.
Genome Res. 2004 Apr;14(4):708-15.
PMID: 15060014; PMC: PMC383317
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.
duplication, deletion, and rearrangement in the mouse and human genomes.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.
PMID: 14500911; PMC: PMC208784
Siepel A, Haussler D.
Computational identification of evolutionarily conserved
Proc. 8th Int'l Conf. on Research in Computational Molecular Biology,