Vertebrate Conservation (phastCons 7 species).


PHASTCONS conservation track downloaded from UCSC based on seven vertebrate species: 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 -

Technical Notes

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 (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018