Understanding "100 Vert Cons" values

[Mandar Kulkarni]

Hi,

I am trying to understand sequence conservation using PhastCons score and new user for UCSC Genome browser. I tried exploring forums and papers but could not get definite answers, so requesting suggestions here.

I performed BLAT on sequence of interest and downloaded 100 vertebrates' conservation score (I guess this is PhastCons score), for track of interest.

Publications say this is probability and I expected these values between 0 and 1. However, these values ranges from -4 to 10 in my case.

Any suggestions what transformation is used here? Is it correct to compare PhastCons score for different sequence fragments from same genome?

Best,

Mandar

[Mandar Kulkarni]

Hi,

It would be great to receive any suggestions from experts.

If question is too basic, please point me to some reading material, as I could not find one.

Also,  I would like to know is there commandline tutorial to get PhastCons7 values for sequences.

Best,

Mandar

[Gerardo Perez]

Hello, Mandar.

Thank you for your interest in the UCSC Genome Browser and for your question about PhastCons scores.

The UCSC 100 Vertebrates values that range from -4 to 10 come from the Basewise Conservation (PhyloP) track, which is turned on by default. The PhastCons track has a range of 0 to 1 and is hidden by default. You can enable it by going to the UCSC 100 Vertebrates Track Settings page and changing the display setting from "hide" to "full":

Regarding whether it is appropriate to compare PhastCons scores for different sequence fragments from the same genome, this falls outside the scope of our mailing list support. You may want to contact the authors of the Siepel et al. 2005 paper (https://genome.cshlp.org/content/15/8/1034) or post your question on Biostars (https://www.biostars.org/), where other scientists and experts can provide further guidance.

We don’t have a command-line tutorial for retrieving PhastCons7 values for sequences, but we can point you toward our makedoc, which details all the operations and programs used to create the hg38 PhastCons 7-way. Keep in mind that this is primarily intended for internal replication. You can find the makedoc below on GitHub:

hg38 PhastCons 7-way makedoc: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/hg38.txt#L4416
hg38 PhastCons 100-way makedoc: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/multiz100way.txt#L1162

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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