PhyloP basewise conservation

Description

PhyloP basewise conservation score derived from Multiz alignment of 44 vertebrate species. This series includes two SGA files, one for all vertebrates and one for placental mammals only.

Source

Files downloaded from UCSC genome browser database:

Samples

From Human Mar. 2006 (NCBI36/hg18) Assembly
Filename Description Feature GEO-ID
1 phylop_vert.sga PhyloP vertebrate 44way (score >= 2) PhyloP -
2 phylop_placental.sga PhyloP placental mammal 44way (score >= 2) 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 ≥2 were considered. The original phyloP score is reflected in the count (5th) field of the SGA files. The real phyloP score values were first dimished by one and then rounded down to the nearest integer:

   counts = int(phyoP_score-1)
USCS also provides phyloP files for Primates. Those were not converted into SGA files, as they primarily contain negative values reflecting accelerated evolution rather than conservation.

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