Difference between PhastCons100way and Multiz100way

[Mériadec Morrier]

Hello,

I was wondering what is the difference between the scores provided by PhastCons100way and Multiz100way because I notice there are not the same ? I thought both would give PhastCons score.

More precisely, when I download the BigWig of PhastCons100way for hg38 (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons100way/hg38.phastCons100way.bw) and compare it to multi100way.txt.gz that I can find in the SQL dump of hg38 (https://hgdownload.gi.ucsc.edu/goldenPath/hg38/database/multiz100way.txt.gz) I don't see the same values (but both are in a [0,1] range).

Thank you very much for your help and for the great work!

Best regards,

Meriadec

[Gerardo Perez]

Hello, Meriadec.

Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.

The PhastCons100way and Multiz100way scores are not the same. The PhastCons100way BigWig file contains phastCons conservation scores, whereas the multiz100way.txt.gz file contains multiple alignment data generated by Multiz. These represent different types of information.

PhastCons is a hidden Markov model–based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. The scores range between 0 and 1 and represent probabilities of negative selection. PhastCons considers not just each individual alignment column, but also its flanking columns. You can find more information in the track description here: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons100way#TRACK_HTML

In contrast, the multiz100way database table (multiz100way.txt.gz) contains alignment data derived from the 100-species multiple sequence alignment produced by the UCSC/Penn State comparative genomics alignment pipeline. The values in this table reflect alignment information and are not phastCons conservation probabilities.

Additional information about the hg38 100-species multiple alignment is available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz100way/README.txt
https://genomewiki.ucsc.edu/index.php?title=Hg38_100-way_conservation_alignment
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons100way/README.txt

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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