PhyloP basewise conservation

Description

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.

Source

Files downloaded from UCSC genome browser database:

Samples

From Zebrafish Jul. 2010 (Zv9/danRer7/) Assembly

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 -

Technical Notes

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.

References

  1. Pollard KS, Hubisz MJ, Siepel A.
    Detection of non-neutral substitution rates on mammalian phylogenies Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363