Vertebrate MultiZ alignment and conservation

[Sara DiNapoli]

Good afternoon,

I was hoping to get some information about the vertebrate MultiZ alignment and conservation track.

- What are the cutoffs that designate whether or not a region has conservation?

- Does the light gray v. dark gray v. black correlate with a cutoff of conservation?

- Is it possible to get the score of the degree of conservation for a specific set of conserved regions?

Thank you in advance for your assistance!

Best,

Sara DiNapoli

Doctoral Candidate, Laboratory of Dr. Yariv Houvras

Weill Cornell Graduate School of Medical Sciences

[Hiram Clawson]

Good Morning Sara:

There is a discussion of the calculations involved in this track
in the description page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons100way

Note the section "Display Conventions and Configuration" on that page:

> Pairwise alignments of each species to the human genome are displayed below
> the conservation histogram as a grayscale density plot (in pack mode) or as
> a wiggle (in full mode) that indicates alignment quality. In dense display
> mode, conservation is shown in grayscale using darker values to indicate
> higher levels of overall conservation as scored by phastCons.


Note the three sections:
PhastCons Conservation
PhyloP Conservation
Conserved Elements

The phastCons method is discussed in:
https://genome.cshlp.org/content/15/8/1034.full

The 'cutoff' is determined in the phastCons HMM prediction of
what is 'conserved' or not conserved. Please note this discussion
from the author of phastCons Adam Siepel regarding this question:

https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/ozbFCmmaCk8


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.

Hiram Clawson
U.C. Santa Cruz Genomics Institute

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