## Description

The exoniphy program identifies evolutionarily conserved protein-coding exons in a multiple alignment using a phylogenetic hidden Markov model (phylo-HMM), a kind of statistical model that simultaneously describes exon structure and exon evolution. This track shows exoniphy predictions for the human May 2004 (hg17), mouse Aug. 2005 (mm7), rat Jun. 2003 (rn3), 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.

## Methods

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).

## References

Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-175 (2004).

Kent, W.J. et al. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. P. Natl. Acad. Sci. USA 100(20), 11484-11489 (2003).

Siepel, A. and Haussler, D. Computational identification of evolutionarily conserved exons. RECOMB '04 (2004).