phyloP base-wise conservation .

PhyloP basewise conservation score derived from Multiz alignment of 27 insect species.

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

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

Sequence-derived:

	Filename	Description	Feature	GEO-ID
1	phylop.sga	PhyloP (27 species) score >= 2)	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 value: 2.0

• 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