PhastCons regional conservation

Description

PhastCons regional 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.

More details about how phastCons conservation scores were computed can be found at:

Note that the original phastCons scores were modified (see below). As a result, these tracks have lower resolution than the origanal phastCons tracks from the UCSC genome browser database.

Source

Files downloaded from UCSC genome browser database:

Samples

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

Filename Description Feature GEO-ID
1 phastcons_vert.sga PhastCons vertebrate 8-way (resolution 10) PHASTCONS -
2 phastcons_fish.sga PhastCons fishes 8-way (resolution 10) PHASTCONS -

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, the following procedure was applied. Each chromosome was partitioned into bins of variable length totalling the same amount of phastCons units. The required amonut of phastCons units per bin is called the resolution. For each bin, a reference position is defined in such a why that the areas before and after the reference position contain approximately the same amount of phastCons units. The SGA files contains the reference positions for each bin. The counts field approximates the total amount phastCons units in the corresponding bin. It is thus invariant and equal to the resolution of phastCons SGA file.

Resolution of the samples (phastCons units): 10

References

  1. Siepel, A. and Haussler, D et al.
    Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005). PMID: 16024819