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<p class="MsoNormal">Hi Thomas,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for the detailed response!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Yes, I was interested in ancestral alleles calls for marmosets. Good to hear that they might be included in an upcoming release.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Murillo<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From:
</span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Thomas Walsh <twalsh@ebi.ac.uk><br>
<b>Date: </b>Friday, August 2, 2024 at 6:13</span><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black"> </span><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">AM<br>
<b>To: </b>Ensembl developers list <dev@ensembl.org><br>
<b>Cc: </b>Murillo Rodrigues <rodrigmu@ohsu.edu><br>
<b>Subject: </b>[EXTERNAL] Re: [ensembl-dev] Ancestral alleles information<o:p></o:p></span></p>
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<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Hi Murillo,<o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Thanks for getting in touch and for your interest in the ancestral alleles data.<o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">I'll try to address each of your questions in turn.<o:p></o:p></span></p>
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<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">How does Ensembl decide which species to call ancestral alleles for?<o:p></o:p></span></p>
</blockquote>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">My understanding is that the original work on this was done as part of the 1000 Genomes Project, with the 6-Primates EPO being used to generate ancestral sequences, from which the ancestral
alleles of human variants were then inferred. If you haven't seen it already, supplementary section 8.3 of the 1000 Genomes paper (
<a href="https://urldefense.com/v3/__https:/doi.org/10.1038/nature15393__;!!Mi0JBg!J8tEMTvdpLfiqOFUA4UkVX3qOwVCd2I_SNfsLKHbMswIb_UZ8k5ZLuI19afw0WNLzbIqxc56ABaR05fb$">
https://doi.org/10.1038/nature15393</a> ) provides some more detail.<o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">The Primates EPO has expanded somewhat since then, and ancestral sequences have continued to be available for the Primates EPO species, with ancestral alleles being extracted from these.<o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Currently, high-coverage primate genome assemblies that are included in comparative analyses are generally included in the Primates EPO, and included in turn in the set of species with ancestral
sequences.<o:p></o:p></span></p>
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<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Can we request new species be added?<o:p></o:p></span></p>
</blockquote>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">In general, there’s no harm in asking. It may or may not be possible to facilitate such a request, but letting us know here or by contacting Ensembl helpdesk (helpdesk@ensembl.org) will at least
help us get a sense of which species users are interested in.<o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">In this particular case, it depends on the species you are interested in and on our capacity to add it. We are currently very constrained in terms of which species we can add to the Primates
EPO, but there are a couple of species — Marmoset (Callithrix jacchus) and Olive baboon (Papio anubis) — which might be feasible to include in an upcoming release, as they are already involved in some comparative analyses but not currently in the Primates
or Mammals EPO. Would you be interested in the ancestral sequences of either of these two species?<o:p></o:p></span></p>
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<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Can I run the ancestral allele pipeline for my own species/EPO alignment of choice?<o:p></o:p></span></p>
</blockquote>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">There's no harm in trying. Results may vary depending on the species and EPO alignment, and on the phylogenetic context of the species within the EPO species tree. Intuitively, there would likely
be a greater number of high-confidence ancestral allele calls for a species nestled among closely related or slowly evolving species, where the sister and ancestral sequences are more likely to be in agreement with each other.<o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Regards,<o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Thomas Walsh.<o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana",sans-serif"><o:p> </o:p></span></p>
<p id="reply-intro"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">On 2024-07-30 02:01, Murillo Rodrigues wrote:<o:p></o:p></span></p>
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<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Hi,<o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif"> <o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">I noticed that Ensembl publishes ancestral alleles for a few species, e.g.
<a href="https://urldefense.com/v3/__https:/ftp.ensembl.org/pub/release-112/fasta/ancestral_alleles/__;!!Mi0JBg!J8tEMTvdpLfiqOFUA4UkVX3qOwVCd2I_SNfsLKHbMswIb_UZ8k5ZLuI19afw0WNLzbIqxc56AIeCxjdt$" target="_blank">
https://ftp.ensembl.org/pub/release-112/fasta/ancestral_alleles/</a><o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif"> <o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">These are calculated based on EPO alignments that are built for subsets of species.<o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif"> <o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">How does Ensembl decide which species to call ancestral alleles for? Can we request new species be added? Can I run the ancestral allele pipeline for my own species/EPO alignment
of choice?<o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif"> <o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Thank your for the help!<o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif"> <o:p></o:p></span></p>
<p class="v1msonormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif">Murillo<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif"><o:p> </o:p></span></p>
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<p class="v1msonormal"><strong><span style="font-family:"Calibri",sans-serif">Thomas Walsh</span></strong><o:p></o:p></p>
<p class="v1msonormal"><strong><span style="font-family:"Calibri",sans-serif">Senior Bioinformatician, Ensembl Compara</span></strong><o:p></o:p></p>
<p class="v1msonormal">European Bioinformatics Institute (EMBL-EBI)<o:p></o:p></p>
<p class="v1msonormal">Wellcome Genome Campus<o:p></o:p></p>
<p class="v1msonormal">Hinxton<o:p></o:p></p>
<p class="v1msonormal">Cambridge CB10 1SD<o:p></o:p></p>
<p class="v1msonormal">United Kingdom<o:p></o:p></p>
<p class="v1msonormal">Email: twalsh@ebi.ac.uk<o:p></o:p></p>
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<p class="v1msonormal"><span style="border:solid windowtext 1.0pt;padding:0in"><img border="0" width="209" height="73" style="width:2.177in;height:.7604in" id="v1Picture_x0020_1" src="cid:~WRD0000.jpg" alt="Image removed by sender."></span><o:p></o:p></p>
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