The exoniphy program identifies evolutionarily conserved protein-coding exons in multiple, aligned sequences 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 Jul. 2003 (hg16), mouse Feb. 2003 (mm3), and rat Jun. 2003 (rn3) genomes, as aligned by the multiz program. These predictions have been mapped to the human May 2004 (hg17) assembly using the liftOver program.
For a description of exoniphy, see Siepel et al. (2004). Multiz is described in Blanchette et al. (2004).
Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-175 (2004).
Siepel, A. and Haussler, D. Computational identification of evolutionarily conserved exons. RECOMB '04 (2004).