Vertebrate Conservation (phastCons 7 species).
PHASTCONS conservation track downloaded from UCSC based on seven vertebrate species:
- chicken (May 2006 (WUGSC 2.1/galGal3), galGal3)
- human (Mar 2006, hg18)
- mouse (Feb 2006, mm8)
- rat (Nov 2004, rn4)
- opossum (Jan 2006, monDom4)
- X. tropicalis (Aug 2005, xenTro2)
- zebrafish (Mar 2006, danRer4)
The original (single-base resolution) phastCons track was modified to conform with format
requirements of the ChIP-Seq software package and compacted to speed up data processing
at a minor expense of precision (see technical notes below).
From G. gallus (Dec 2015 Gallus_gallus-5.0/galGal5).
| || Filename || Description || Feature || GEO-ID |
| 1 || phastcons_new.sga || PHASTCONS (7 species) || PHASTCONS || - |
This is a compacted version of the phastCons track provided by UCSC. The original
version provides conservation probabilities for single bases. This version provides
integer scores between 1 and 5 for short regions where PhastCons scores consistently
are greater or equal to 0.5. The integer scores are the rounded sums of the phastCons
probabilities within such a regions. Larger regions with consistently high phastCons
probabilites are cut into shorter chunks with sum of probabilites not exceeding 5.
The single genomic position given in the SGA file corresponds to the
probability-weighted average position (center of gravity) of the corresponding
conserved region. For more details, see directly the Perl script available from our FTP
site (URL given below).
At the time this series was generated, UCSC didn't provide conservation tracks
for assembly galGal5. We therefore used the phastCons track for galGal3 as starting data.
The WIG file was compacted and converted into SGA format using custom scripts available at
Original coordinates for galGal3 were converted to galGal5 using the liftOver program
from UCSC available from
BED-to-SGA conversion was carried out using bed2sga
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Genome Res. 2005 Aug;15(8):1034-50. Epub 2005 Jul 15.