PhyloP score

[sof...@gmail.com]

I used Alamut version 2.6 to get the PhyloP score for some variants, and I know PhyloP scores in the Alamut report are obtained from UCSC Genome Browser. Now I need to know how many species and which ones are taken into consideration.

I thank you in advance.

Best regards,

Sofia Maia

Sent from Windows Mail

[Jonathan Casper]

Hello Sofia,

Thank you for your question about identifying the source of the PhyloP data that you obtained from Alamut. Are you able to get any further details from Alamut about the source of the PhyloP scores? The exact UCSC track identifier in particular would be very helpful. We provide multiple conservation tracks for different assemblies, and each one involves different collections of species. Without knowing which conservation track was used, we can't give you the information that you request.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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[Sofia Maia]

Hi Jonathan,

Thank you for your email.
Alamut has already answered my question.

They use a 44-vertebrate alignment (UCSC 46-vertebrate alignment, except baboon and wallaby).

Best regards,

Sofia