[ensembl-dev] where to find GERP scores? How to read EMF files?

Julie Sullivan julie.sullivan at gmail.com
Mon Jul 6 15:09:09 BST 2020

On that page is a gerp score GERP: 1.27. Where can I download that GERP

I found this: https://www.ensembl.org/Help/Faq?id=221

Which says to get the gerp scores from an EMF file. I am unfamiliar with
this file type. (apparently emf is also a image file type, so google didn't


The EMF file looks like this:

##FORMAT (compara)
##DATE Fri Feb 21 15:26:12 2020
# Alignments: 103 eutherian mammals EPO-Low-Coverage
# Region: Homo sapiens chromosome:GRCh38:10:1:133797422:1
# File 1

SCORE 103 eutherian mammals GERP Conservation Scores
ID 18230001887772
aAAaaaaaaAaAAGGGGA-AAA---A--AAA-AA---CC-A -1.03 <-- which position is this
score for?
cCCccccccCcCCCCCCC-CCC---T--CCC-TC---TT-C -1.97

1. is this file the right place to get the GERP scores listed on the
2. Does each line represent a position? So "-1.03" would be the score for
position chr10:1? Or is there a way to find out which positions are being
described? Or am I reading this file wrong? Because position 1 doesn't make
a lot of sense but I don't see another number.

Thank you!


I also tried the Perl API and this file but was not successful:

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