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<!--StartFragment--><p class="MsoNormal"><b>Gene Model Annotation 1.8.3 of the <i>X.
laevis</i> 9.1 Genome Build<o:p></o:p></b></p><p class="MsoNormal">The latest annotation of the <i>X. laevis</i> 9.1 genome is ready! </p><p class="MsoNormal">This release only includes updating the gene symbol
of existing gene models. </p><p class="MsoNormal">The files for
this annotation release, GFFs and FASTA, can be downloaded from the <a href="http://www.xenbase.org/other/static/ftpDatafiles.jsp">Xenbase FTP page</a>,
under the <i>X. laevis</i> genome assemblies
and gene models category. </p><p class="MsoNormal"><b>Xenbase updates to <i>X. laevis</i>
Gene Model Symbol Annotation: Merging and Validation<o:p></o:p></b></p><p class="MsoNormal">Gene model symbol annotations were
merged and validated from the following sources: </p></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><p class="MsoNormal">1) Xenopus Genome Consortium
(XGC)</p></div><div><p class="MsoNormal">2) Xenbase (<a href="http://www.xenbase.org">www.xenbase.org</a>)</p></div><div><p class="MsoNormal">3) Dr. Anne-Hélène Monsoro-Burq (<a href="mailto:anne-helene.monsoro-burq@curie.fr">anne-helene.monsoro-burq@curie.fr</a>)
and Jean-Louis
Plouhinec </p></div><div><p class="MsoNormal">4) Dr. Emil Karaulanov (<a href="mailto:E.Karaulanov@imb-mainz.de">E.Karaulanov@imb-mainz.de</a>). </p></div></blockquote><div><p class="MsoNormal">These
combined efforts have named 27325 of the 45099 (61%) gene models, an increase
of 5624 named models from the original XGC annotation.</p><div><br></div><p class="MsoNormal">The compendium of provisional
annotation data from all groups was aggregated and analyzed to identify and
verify symbol assignment to gene models. </p><p class="MsoNormal"><ul><li>Annotations that were congruent between all annotators were
automatically assigned.</li><li>For all other cases, each annotation was assessed to
identify the human equivalent. </li><li>For each of these annotations, a low level,
automated symbol-matching synteny analysis was performed between the human and <i>Xenopus</i> loci. </li><li>The symbols from up to
fifteen neighbors, both upstream and downstream of the target gene model, in
both species were used. </li><li>Gene symbols that were confirmed by at least low level
synteny were considered verified and were preferred over non-synteny
annotations. </li><li>In cases where a model had more than one annotation with synteny
support, manual validation was used to identify the correct assignment (324 models). </li><li>For models where no annotations had synteny support, assignments from the XGC
and Xenbase were used. </li><li>Differences between the XGC and Xenbase were resolved
via manual annotation (>400 models).</li><li>All 1709 models annotated with an <i>X. tropicalis</i> 9.0 gene model ID are
provisional and will require future work.</li></ul></p><p class="MsoNormal">Any questions can be directed to Joshua Fortriede (<a href="mailto:Joshua.Fortried@cchmc.org">Joshua.Fortried@cchmc.org</a>) at Xenbase.</p><p class="MsoNormal"><br></p></div><br><div apple-content-edited="true">
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