https://wiki.biouml.org/index.php?action=history&feed=atom&title=Ensembl 2026-04-12T18:58:59Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Ensembl&diff=4720&oldid=prev 2013-06-27T06:15:29Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 06:15, 27 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>{{stub}}</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>{{stub}}</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases].</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases].</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Ensembl database is available for different species. Usually [[BioUML]] installation contains Ensembl for human, mouse and rat, though it's possible to install other species as well. The installed Ensembl databases appear under the '''Databases''' tab.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">The </ins>Ensembl database is available for different species. Usually <ins class="diffchange diffchange-inline">the </ins>[[BioUML]] installation contains Ensembl <ins class="diffchange diffchange-inline">data </ins>for human, mouse and rat, though it's possible to install other species as well. The installed Ensembl databases appear under the '''Databases''' tab.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The following collections are available in BioUML Ensembl database:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The following collections are available in <ins class="diffchange diffchange-inline">a </ins>BioUML Ensembl database:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Data''': informational data elements. Information about them is available in [[information box]]. These collections can be searched using [[Lucene search]].</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* '''Data''': informational data elements. Information about them is available in [[information box]]. These collections can be searched using [[Lucene search]].</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''gene''': list of all genes with annotation;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>** '''gene''': list of all genes with annotation;</div></td></tr> </table>

Stan.lo@dote.ru https://wiki.biouml.org/index.php?title=Ensembl&diff=4696&oldid=prev 2013-06-26T08:24:12Z

<p>+<a href="/index.php/Category:Databases" title="Category:Databases">Category:Databases</a></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 08:24, 26 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 24:</td> <td colspan="2" class="diff-lineno">Line 24:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==External links==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==External links==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ensembl.org/ Ensemble official website]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ensembl.org/ Ensemble official website]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Category:Databases]]</ins></div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=Ensembl&diff=4687&oldid=prev 2013-06-26T08:14:13Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 08:14, 26 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>{{stub}}</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>{{stub}}</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases].</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases].</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Presently, there are </del>human, mouse and rat Ensembl <del class="diffchange diffchange-inline">data included in the BioUML platform, separately listed </del>under the '''Databases''' tab<del class="diffchange diffchange-inline">. The human data are from database version 61.37f (assembly GRCh37.p3, February 2009), the mouse data refer to database version 65.37 and the rat data version is 65.34</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Ensembl database is available for different species. Usually [[BioUML]] installation contains Ensembl for </ins>human, mouse and rat<ins class="diffchange diffchange-inline">, though it's possible to install other species as well. The installed </ins>Ensembl <ins class="diffchange diffchange-inline">databases appear </ins>under the '''Databases''' tab.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The <del class="diffchange diffchange-inline">alignment of genes and other genomic </del>data <del class="diffchange diffchange-inline">against a reference genome </del>can be <del class="diffchange diffchange-inline">viewed </del>as <del class="diffchange diffchange-inline">data tracks </del>in [[genome browser]].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The <ins class="diffchange diffchange-inline">following collections are available in BioUML Ensembl database:</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Data''': informational </ins>data <ins class="diffchange diffchange-inline">elements. Information about them is available in [[information box]]. These collections </ins>can be <ins class="diffchange diffchange-inline">searched using [[Lucene search]].</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** '''gene''': list of all genes with annotation;</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** '''variation''': list of all variations with annotation (available if variation database is installed)</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Sequences''': list of chromosomes represented </ins>as <ins class="diffchange diffchange-inline">{{Type link|sequence|sequence elements}}. They can be opened </ins>in [[genome browser]]<ins class="diffchange diffchange-inline">.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Tracks''': list of {{Type link|track}}s, which can be added to [[genome browser]]:</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** '''Karyotype''': karyotype (chromosome bands) display;</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** '''GC content''': graph displaying the local density of GC nucleotides;</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** '''Genes''': genes with exon-intron structure (including non-coding, pseudogenes, etc.);</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** '''ExtendedGeneTrack''': an alternative gene track where all genes are displayed in single line;</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** '''Repeats''': repeats regions (like Alu);</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** '''Variations''': SNPs and other known genomic variations (available if variation database is installed)</ins>.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==See also==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Databases]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Databases]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*[[<del class="diffchange diffchange-inline">Search tools</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*[[<ins class="diffchange diffchange-inline">Lucene search</ins>]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Genome browser]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Genome browser]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Ensembl installation]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Ensembl installation]]</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=Ensembl&diff=4685&oldid=prev 2013-06-26T07:59:04Z

<p>+<a href="/index.php/Ensembl_installation" title="Ensembl installation">Ensembl installation</a></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:59, 26 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 9:</td> <td colspan="2" class="diff-lineno">Line 9:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Search tools]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Search tools]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Genome browser]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Genome browser]]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*[[Ensembl installation]]</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==External links==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==External links==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ensembl.org/ Ensemble official website]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ensembl.org/ Ensemble official website]</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=Ensembl&diff=4684&oldid=prev 2013-06-26T07:57:43Z

<p>‎<span dir="auto"><span class="autocomment">See also</span></span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:57, 26 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Databases]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Databases]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Search tools]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Search tools]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*[[<del class="diffchange diffchange-inline">Genome_browser</del>]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*[[<ins class="diffchange diffchange-inline">Genome browser</ins>]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==External links==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==External links==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ensembl.org/ Ensemble official website]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ensembl.org/ Ensemble official website]</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=Ensembl&diff=4682&oldid=prev 2013-06-26T05:41:17Z

<p>Stan.lo@dote.ru moved page <a href="/index.php/Ensemble" class="mw-redirect" title="Ensemble">Ensemble</a> to <a href="/index.php/Ensembl" title="Ensembl">Ensembl</a>: typo in the title</p> <table class='diff diff-contentalign-left'> <tr style='vertical-align: top;'> <td colspan='1' style="background-color: white; color:black;">← Older revision</td> <td colspan='1' style="background-color: white; color:black;">Revision as of 05:41, 26 June 2013</td> </tr></table>

Stan.lo@dote.ru https://wiki.biouml.org/index.php?title=Ensembl&diff=4681&oldid=prev 2013-06-26T05:39:51Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 05:39, 26 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">{{stub}}</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases].</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases].</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Presently, there are human, mouse and rat Ensembl data included in the BioUML platform, separately listed under the '''Databases''' tab. The human data are from database version 61.37f (assembly GRCh37.p3, February 2009), the mouse data refer to database version 65.37 and the rat data version is 65.34.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Presently, there are human, mouse and rat Ensembl data included in the BioUML platform, separately listed under the '''Databases''' tab. The human data are from database version 61.37f (assembly GRCh37.p3, February 2009), the mouse data refer to database version 65.37 and the rat data version is 65.34.</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Databases]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Databases]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Search tools]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*[[Search tools]]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*[[Genome_browser]]</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==External links==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==External links==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ensembl.org/ Ensemble official website]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ensembl.org/ Ensemble official website]</div></td></tr> </table>

Stan.lo@dote.ru https://wiki.biouml.org/index.php?title=Ensembl&diff=4678&oldid=prev 2013-06-25T12:07:41Z

<p>from GX manual</p> <p><b>New page</b></p><div><br /> The Ensembl database provides annotation of genes from the [http://www.ensembl.org/index.html Ensembl genome databases].<br /> Presently, there are human, mouse and rat Ensembl data included in the BioUML platform, separately listed under the '''Databases''' tab. The human data are from database version 61.37f (assembly GRCh37.p3, February 2009), the mouse data refer to database version 65.37 and the rat data version is 65.34.<br /> <br /> The alignment of genes and other genomic data against a reference genome can be viewed as data tracks in [[genome browser]].<br /> <br /> ==See also==<br /> *[[Databases]]<br /> *[[Search tools]]<br /> <br /> ==External links==<br /> * [http://www.ensembl.org/ Ensemble official website]</div>

Stan.lo@dote.ru