http://wiki.biouml.org/index.php?title=Track_(element_type)&feed=atom&action=historyTrack (element type) - Revision history2024-03-29T15:05:45ZRevision history for this page on the wikiMediaWiki 1.20.3http://wiki.biouml.org/index.php?title=Track_(element_type)&diff=4723&oldid=prevStan.lo@dote.ru at 06:29, 27 June 20132013-06-27T06:29:18Z<p></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 06:29, 27 June 2013</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Stub|pictures and more detailed track types information}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Stub|pictures and more detailed track types information}}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Description ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Description ===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>'''Track''' is an element which contains genomic features (or '''sites'''). There are various implementations of tracks which provide the unified track interface for different sources including Ensembl database, SQL database for user uploaded data, BAM files, remote DAS servers and so on.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''Track''' is an element which contains genomic features (or '''sites'''). There are various implementations of tracks which provide the unified track interface for different sources including <ins class="diffchange diffchange-inline">the </ins>Ensembl database, SQL database for user uploaded data, BAM files, remote DAS servers and so on.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </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 main function of the track is to provide list of sites located in specified region of <del class="diffchange diffchange-inline">the </del>specified {{Type link|sequence}}. Each site has genomic coordinates, strand and a number of annotation fields. Also every track has a '''TrackViewBuilder''' associated with it, which controls how these sites will be drawn in the [[genome browser]]. Thanks to this different tracks are displayed in different ways.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The main function of the track is to provide <ins class="diffchange diffchange-inline">a </ins>list of sites located in <ins class="diffchange diffchange-inline">a </ins>specified region of <ins class="diffchange diffchange-inline">a </ins>specified {{Type link|sequence}}. Each site has genomic coordinates, strand and a number of annotation fields. Also every track has a '''TrackViewBuilder''' associated with it, which controls how these sites will be drawn in the [[genome browser]]. Thanks to this<ins class="diffchange diffchange-inline">, </ins>different tracks are displayed in different ways.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Most of the tracks are associated with some sequences collection. In this case you can double click on the track to open it in the [[genome browser]]. Alternatively you can first open the {{Type link|sequence}} in the genome browser, then drag the track on it to add it to the view.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Most of the tracks are associated with some sequences collection. In this case you can double click on the track to open it in the [[genome browser]]. Alternatively you can first open the {{Type link|sequence}} in the genome browser, then drag the track on it to add it to the view.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </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>Some tracks can be opened as [[table document]] using [[File:WebAction-tree-open_table-icon.png]] '''Open as table''' context action. In this case list of all sites in the track will be displayed in tabular form with the ability to sort, filter and so on.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Some tracks can be opened as <ins class="diffchange diffchange-inline">a </ins>[[table document]] using <ins class="diffchange diffchange-inline">the </ins>[[File:WebAction-tree-open_table-icon.png]] '''Open as table''' context action. In this case <ins class="diffchange diffchange-inline">a </ins>list of all sites in the track will be displayed in tabular form with the ability to sort, filter and so on.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </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>Some tracks also work as collections of sequences. Every sequence in this collection corresponds to <del class="diffchange diffchange-inline">the </del>track site. These sequences can be opened in genome browser as well.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Some tracks also work as collections of sequences. Every sequence in this collection corresponds to <ins class="diffchange diffchange-inline">a </ins>track site. These sequences can be opened in <ins class="diffchange diffchange-inline">the </ins>genome browser as well.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Tracks can be imported from many different file formats including [[SAM or BAM alignment file|BAM]], [[BED format|BED]], [[General Feature Format|GFF]], [[VCF format|VCF]] and many more. Tracks are used and produced by numerous analysis methods.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Tracks can be imported from many different file formats including [[SAM or BAM alignment file|BAM]], [[BED format|BED]], [[General Feature Format|GFF]], [[VCF format|VCF]] and many more. Tracks are used and produced by numerous analysis methods.</div></td></tr>
<tr><td colspan="2"> </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"> </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;">==See also==</ins></div></td></tr>
<tr><td colspan="2"> </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 colspan="2"> </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]]</ins></div></td></tr>
</table>Stan.lo@dote.ruhttp://wiki.biouml.org/index.php?title=Track_(element_type)&diff=4701&oldid=prevLan@dote.ru: Created page with "{{Element type|track|ru.biosoft.bsa.Track}} {{Stub|pictures and more detailed track types information}} === Description === '''Track''' is an element which contains genomic fe..."2013-06-26T09:02:33Z<p>Created page with "{{Element type|track|ru.biosoft.bsa.Track}} {{Stub|pictures and more detailed track types information}} === Description === '''Track''' is an element which contains genomic fe..."</p>
<p><b>New page</b></p><div>{{Element type|track|ru.biosoft.bsa.Track}}<br />
{{Stub|pictures and more detailed track types information}}<br />
=== Description ===<br />
'''Track''' is an element which contains genomic features (or '''sites'''). There are various implementations of tracks which provide the unified track interface for different sources including Ensembl database, SQL database for user uploaded data, BAM files, remote DAS servers and so on.<br />
<br />
The main function of the track is to provide list of sites located in specified region of the specified {{Type link|sequence}}. Each site has genomic coordinates, strand and a number of annotation fields. Also every track has a '''TrackViewBuilder''' associated with it, which controls how these sites will be drawn in the [[genome browser]]. Thanks to this different tracks are displayed in different ways.<br />
<br />
Most of the tracks are associated with some sequences collection. In this case you can double click on the track to open it in the [[genome browser]]. Alternatively you can first open the {{Type link|sequence}} in the genome browser, then drag the track on it to add it to the view.<br />
<br />
Some tracks can be opened as [[table document]] using [[File:WebAction-tree-open_table-icon.png]] '''Open as table''' context action. In this case list of all sites in the track will be displayed in tabular form with the ability to sort, filter and so on.<br />
<br />
Some tracks also work as collections of sequences. Every sequence in this collection corresponds to the track site. These sequences can be opened in genome browser as well.<br />
<br />
Tracks can be imported from many different file formats including [[SAM or BAM alignment file|BAM]], [[BED format|BED]], [[General Feature Format|GFF]], [[VCF format|VCF]] and many more. Tracks are used and produced by numerous analysis methods.</div>Lan@dote.ru