[ensembl-dev] Question: why can't I find GERP score in emf file?

Tang, Haiming ningzhithm at gmail.com
Tue Oct 7 16:48:46 BST 2014

Thank you so much Stephen. I really appreciated the time you spent with me.

On Tue, Oct 7, 2014 at 2:07 AM, Stephen Fitzgerald <stephenf at ebi.ac.uk>

> Hi Haiming, we no longer produce gerp scores for the alignments containing
> the smaller set of mammals (16 species in e76, and 17 in e77).
> We do produce gerp scores for the larger set of mammal alignments (38
> species in e76 and 39 in e77), which contain all of the (high quality
> assembly) species present in the smaller set plus extra (lower quality (2X)
> assembly) species. The EMF files for the epo_16_eutherian mammals (e76)
> contain no extra information compared with the MAF files for the same
> alignments, and have therefore not been generated for e77.
> ftp://ftp.ensembl.org/pub/release-77/emf/ensembl-compara/
> If you need the gerp scores for mammals (for e76) use the scores from the
> 38 mammals:
> ftp://ftp.ensembl.org/pub/release-76/emf/ensembl-compara/epo_38_eutherian/
> The scores are generated from the same blocks present in the 16 species,
> but should give a more accurate value for the constraint at any position
> due to the extra information (provided by 22 extra species) present in the
> larger alignments. Regions under constraint (constrained elements) defined
> by the 38 mammals will be very similar to those that would have been
> defined for the 16 mammals, but should be more fine-grained in their
> boundaries.
> Hope that helps,
> Stephen.
> On Mon, 6 Oct 2014, Tang, Haiming wrote:
>  Dear group,
>> I tried to get the conservation scores (GERP scores) for nucleotides in
>> whole genome alignments.
>> So I  followed "http://uswest.ensembl.org/Help/Faq?id=221" to download
>> the emf files for multiple species alignments
>> from ftp site: ftp://ftp.ensembl.org/pub/release-76/emf/ensembl-
>> compara/epo_16_eutherian/
>> But why can't I find GERP score in these emf files?
>> Thanks
>> Haiming
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