phyloP base-wise conservation .

PhyloP basewise conservation score derived from Multiz alignment of 8 vertebrate species. This series includes two SGA files, one for all vertebrates and one for fishes only.

• Raw data was downloaded from: UCSC vertebrate and fish
• Input file format: WIG
• Download date: n/a

From D. rerio (July 2010 Zv9/danRer7).

Sequence-derived:

	Filename	Description	Feature	GEO-ID
1	phylop_vert.sga	PhyloP vertebrate 8way (score >= 2)	PhyloP	-
2	phylop_fish.sga	PhyloP fish 8way (score >= 1.5)	PhyloP	-

The sources files are in WIG fixedStep format. Conversion into SGA was carried out with an ad hoc Perl script. In order to keep the SGA files reasonably compact, only positions with phyloP scores greater than a threshold value t were considered. The original real-valued scores were first dimished by t-1 and then rounded down to the nearest integer:

	  counts = int(phyoP_score-t+1)
	

The modified phyloP score is given in the count (5th) field of the SGA files.
Threshold values: 2.0 for vertebrate, 1.5 for fishes.

• Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A
  Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. doi: 10.1101/gr.097857.109. Epub 2009 Oct 26. 19858363