Exoniphy Track Settings
 
Exoniphy Human/Mouse/Rat/Dog   (All Genes and Gene Predictions tracks)

Display mode:   

Color track by codons: Help on codon coloring

Show codon numbering:

Display data as a density graph:

View table schema
Data last updated: 2009-12-29

Description

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.

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.

Acknowledgments

Thanks to Melissa Hubisz of the Siepel lab at Cornell University for producing these predictions.

References

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. Evolution's cauldron: 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 exons. RECOMB '04. 2004.