PhastCons 15-way, Genome Conservation Scores.

This track shows a measure of evolutionary conservation in twelve Drosophila species, mosquito, honeybee and red flour beetle, based on a phylogenetic hidden Markov model (phastCons). Multiz alignments of the following assemblies were used to generate this annotation:

• D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3)
• D. simulans Apr. 2005 (droSim1)
• D. sechellia Oct. 2005 (droSec1)
• D. yakuba Nov. 2005 (droYak2)
• D. erecta Feb. 2006 (droEre2)
• D. ananassae Feb. 2006 (droAna3)
• D. pseudoobscura Feb. 2006 (dp4)
• D. persimilis Oct. 2005 (droPer1)
• D. willistoni Feb. 2006 (droWil1)
• D. virilis Feb. 2006 (droVir3)
• D. mojavensis Feb. 2006 (droMoj3)
• D. grimshawi Feb. 2006 (droGri2)
• A. gambiae Feb. 2003 (anoGam1)
• A. mellifera May. 2005 (apiMel3)
• T. castaneum Sep. 2005 (triCas2)

• Raw data was downloaded from: UCSC Genome Browser FTP
• Input file format: TXT
• Download date: n/a

From D. melanogaster (Apr 2006 BDGP R5/dm3).

Sequence-derived:

	Filename	Description	Feature	GEO-ID
1	phastcons.sga	PHASTCONS 15-way	PHASTCONS	-

Best-in-genome pairwise alignments were generated for each species using blastz, followed by chaining and netting.

The phastCons parameters for the 15-way Drosophila annotations are: expected-length = 23.8; target-coverage = 0.393; rho is set to the default value = 0.3.

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM.

PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.

• Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D
  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. Epub 2005 Jul 15. 16024819