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<p>Dear Ben,</p>
<p>Age-of-Base is not currently stored in Compara databases, but if you have <span style="font-family: 'courier new', courier, monospace;">bigBedToBed</span> installed, you can fetch current Age-of-Base data for your region of interest as follows:</p>
<p style="padding-left: 40px;"><span style="font-family: 'courier new', courier, monospace;">bigBedToBed https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/compara/Hsap_ages_2072_111.bb \</span><br /><span style="font-family: 'courier new', courier, monospace;"> -chrom=19 -start=1581090 -end=1581269 Hsap_ages_19_1581091_1581269.bed</span></p>
<p>The Age-of-Base file is periodically updated, so it may be no harm to keep an eye out for updated versions of the file at: <a href="https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/compara/">https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/compara/</a></p>
<p>All the best,</p>
<p>Tom Walsh.</p>
<p><br /></p>
<p id="reply-intro">On 2024-04-09 16:21, Benoit Ballester wrote:</p>
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<div>Dear Ensembl, </div>
<div> </div>
<div>I am trying to get the "age of base" as described here :</div>
<div><a href="https://www.ensembl.org/info/genome/compara/age_of_base.html" target="_blank" rel="noopener noreferrer">https://www.ensembl.org/info/genome/compara/age_of_base.html</a> </div>
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<div>Basically, for a slice like this, I'd like to get those "age". </div>
<div>$slice = $hsap_slice_adaptor->fetch_by_region( 'toplevel', '19' , '1581091','1581269');</div>
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<div> </div>
<div>It has been a while since I last used the ensembl API (prob ~v60), so I wonder if I could get those values from a core slice (which I doubt), most likely from a compara object, but which one ? Is this something stored in the compara db for human, or computed on the fly from a multiple alignment objet ?</div>
<div> </div>
<div>The Doxygen doc is not of much of any help for me I am afraid, as I can't get much info there. </div>
<div> </div>
<div>Any embryo of code to get me on track would be must appreciated. </div>
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<div>I am on version 111 of core and compara. </div>
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<div>Thanks,</div>
<div> </div>
Ben<br />
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">--<br />Benoît Ballester, PhD<br />Inserm U1090, TAGC<br />Campus de Luminy<br />13288 Marseille Cedex 9<br />France<br />+33 4 91 82 87 28<br />(1st) <a href="mailto:benoit.ballester@inserm.fr" rel="noreferrer">benoit.ballester@inserm.fr</a><br />(2nd) <a href="mailto:benoit.ballester@univ-amu.fr" rel="noreferrer">benoit.ballester@univ-amu.fr</a> </div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">ReMap2022: <a href="http://remap.univ-amu.fr/" target="_blank" rel="noopener noreferrer">http://remap.univ-amu.fr/</a></div>
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<div class="pre" style="margin: 0; padding: 0; font-family: monospace">_______________________________________________<br />Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br />Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" target="_blank" rel="noopener noreferrer">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br />Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank" rel="noopener noreferrer">http://www.ensembl.info/</a></div>
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<p class="v1MsoNormal"><strong><span>Thomas Walsh</span></strong></p>
<p class="v1MsoNormal"><strong>Senior Bioinformatician, Ensembl Compara</strong></p>
<p class="v1MsoNormal"><span>European Bioinformatics Institute (EMBL-EBI)</span></p>
<p class="v1MsoNormal"><span>Wellcome Genome Campus</span></p>
<p class="v1MsoNormal"><span>Hinxton</span></p>
<p class="v1MsoNormal"><span>Cambridge CB10 1SD</span></p>
<p class="v1MsoNormal"><span>United Kingdom</span></p>
<p class="v1MsoNormal"><span>Email: twalsh@ebi.ac.uk</span></p>
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