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:
- Input file format: WIG
- Download date: n/a
From D. rerio (July 2010 Zv9/danRer7).
| || 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
were considered. The original real-valued scores
were first dimished by t
-1 and then rounded down to the
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.