<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div>Hi Tom,</div><div><br></div><div>Thanks for the prompt reply. </div><div><br></div><div>What would be the description of col4 and col5 ? </div><div><br></div><div>Col4 <span style="caret-color: rgb(47, 255, 18); color: rgb(47, 255, 18); font-family: Menlo; font-size: 13px; background-color: rgba(0, 0, 0, 0.9);">Hsap-Mfas-Mmul-Ptro</span> are the species in which the substitution occurred ?</div><div>Col5 is a score ? age in Mya?</div><div><br></div><div>Thanks </div><div><br></div><div><p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581102<span class="Apple-tab-span" style="white-space:pre"> </span>1581103<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Mfas-Mmul-Ptro[4]<span class="Apple-tab-span" style="white-space:pre"> </span>319<span class="Apple-tab-span" style="white-space:pre"> </span>81,81,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581120<span class="Apple-tab-span" style="white-space:pre"> </span>1581121<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Mfas-Mmul-Ptro[4]<span class="Apple-tab-span" style="white-space:pre"> </span>319<span class="Apple-tab-span" style="white-space:pre"> </span>81,81,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581138<span class="Apple-tab-span" style="white-space:pre"> </span>1581139<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Mfas-Mmul-Ptro[4]<span class="Apple-tab-span" style="white-space:pre"> </span>319<span class="Apple-tab-span" style="white-space:pre"> </span>81,81,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581150<span class="Apple-tab-span" style="white-space:pre"> </span>1581151<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Ptro[2]<span class="Apple-tab-span" style="white-space:pre"> </span>92<span class="Apple-tab-span" style="white-space:pre"> </span>23,23,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581153<span class="Apple-tab-span" style="white-space:pre"> </span>1581154<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Ptro[2]<span class="Apple-tab-span" style="white-space:pre"> </span>92<span class="Apple-tab-span" style="white-space:pre"> </span>23,23,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581174<span class="Apple-tab-span" style="white-space:pre"> </span>1581175<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Mfas-Mmul-Ptro[4]<span class="Apple-tab-span" style="white-space:pre"> </span>319<span class="Apple-tab-span" style="white-space:pre"> </span>81,81,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581186<span class="Apple-tab-span" style="white-space:pre"> </span>1581187<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Mfas-Mmul-Ptro[4]<span class="Apple-tab-span" style="white-space:pre"> </span>319<span class="Apple-tab-span" style="white-space:pre"> </span>81,81,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581189<span class="Apple-tab-span" style="white-space:pre"> </span>1581190<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Mfas-Mmul-Ptro[4]<span class="Apple-tab-span" style="white-space:pre"> </span>319<span class="Apple-tab-span" style="white-space:pre"> </span>81,81,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581219<span class="Apple-tab-span" style="white-space:pre"> </span>1581220<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Mfas-Mmul-Ptro[4]<span class="Apple-tab-span" style="white-space:pre"> </span>319<span class="Apple-tab-span" style="white-space:pre"> </span>81,81,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581249<span class="Apple-tab-span" style="white-space:pre"> </span>1581250<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Ptro[2]<span class="Apple-tab-span" style="white-space:pre"> </span>92<span class="Apple-tab-span" style="white-space:pre"> </span>23,23,255</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal; color: rgb(47, 255, 18); background-color: rgba(0, 0, 0, 0.9);"><span style="font-variant-ligatures: no-common-ligatures">19<span class="Apple-tab-span" style="white-space:pre"> </span>1581258<span class="Apple-tab-span" style="white-space:pre"> </span>1581259<span class="Apple-tab-span" style="white-space:pre"> </span>Hsap-Mfas-Mmul-Ptro[4]<span class="Apple-tab-span" style="white-space:pre"> </span>319<span class="Apple-tab-span" style="white-space:pre"> </span>81,81,255</span></p></div><br><div>
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div>--</div><div>Benoît Ballester, PhD<br>INSERM U1090 TAGC<br>Aix-Marseille-Université<br>Parc Scientifique de Luminy<br>13288 Marseille Cedex 9. France<br><br>(1st) benoit.ballester@inserm.fr<br>(2nd) benoit.ballester@univ-amu.fr<br>ReMap: http://remap.univ-amu.fr/ </div></div></div></div>
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<div><br><blockquote type="cite"><div>On 10 Apr 2024, at 15:50, Thomas Walsh <twalsh@ebi.ac.uk> wrote:</div><br class="Apple-interchange-newline"><div>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div style="font-size: 10pt; font-family: Verdana,Geneva,sans-serif"><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>
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<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>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>
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<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>
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<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>
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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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<td valign="top" width="368"><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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