Difference between revisions of "Genome browser"
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| − | The BioUML genome browser is a graphical interface for displaying and browsing sequences with several tracks within one document. BioUML allows the user to combine sequences and tracks from different databases and data sources into one unified representation. For example, it is possible to get genomic sequences and gene tracks from [[Ensembl]] and add tracks from the user ChIP-seq data. | + | The BioUML genome browser <ref>Valeev T., Yevshin I., Kolpakov F. BioUML Genome Browser. Virtual Biology, 2013, V. 1. {{doi|10.12704/vb/e8}}</ref> is a graphical interface for displaying and browsing sequences with several tracks within one document. BioUML allows the user to combine sequences and tracks from different databases and data sources into one unified representation. For example, it is possible to get genomic sequences and gene tracks from [[Ensembl]] and add tracks from the user ChIP-seq data. |
[[File:Sequence_in_genome_browser_web.png|thumb|A sequence opened in the genome browser of BioUML web edition]] | [[File:Sequence_in_genome_browser_web.png|thumb|A sequence opened in the genome browser of BioUML web edition]] | ||
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When a sequence has been opened, the user can see the track names and the track content aligned according to the genomic positions along the chromosome selected. In the case of gene track, the gene names are displayed above a representation of the exon/introne structure of genes. | When a sequence has been opened, the user can see the track names and the track content aligned according to the genomic positions along the chromosome selected. In the case of gene track, the gene names are displayed above a representation of the exon/introne structure of genes. | ||
With the zoom buttons in the [[general control panel]] above the user can flexibly change the scale on which the sequence is viewed - from the nucleotide level to the level of the complete chromosome. Tracks can be hidden from the view by unchecking the options under the '''Tracks''' tab in the [[Viewparts|viewparts area]] below. There's also a number of options available for changing the appearance of each track (the '''Options''' buttons). | With the zoom buttons in the [[general control panel]] above the user can flexibly change the scale on which the sequence is viewed - from the nucleotide level to the level of the complete chromosome. Tracks can be hidden from the view by unchecking the options under the '''Tracks''' tab in the [[Viewparts|viewparts area]] below. There's also a number of options available for changing the appearance of each track (the '''Options''' buttons). | ||
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| + | ==References== | ||
| + | <references/> | ||
==See also== | ==See also== | ||
Latest revision as of 11:34, 1 July 2013
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The BioUML genome browser [1] is a graphical interface for displaying and browsing sequences with several tracks within one document. BioUML allows the user to combine sequences and tracks from different databases and data sources into one unified representation. For example, it is possible to get genomic sequences and gene tracks from Ensembl and add tracks from the user ChIP-seq data.
The genome browser is launched in the document pane whenever a sequence (chromosome) element is opened from the Ensembl database in the repository pane. While opening, the genome browser will prompt the user to specify the tracks to be added (currently there are six of them, all selected by dafault in the Add tracks to genome browser dialog).
When a sequence has been opened, the user can see the track names and the track content aligned according to the genomic positions along the chromosome selected. In the case of gene track, the gene names are displayed above a representation of the exon/introne structure of genes. With the zoom buttons in the general control panel above the user can flexibly change the scale on which the sequence is viewed - from the nucleotide level to the level of the complete chromosome. Tracks can be hidden from the view by unchecking the options under the Tracks tab in the viewparts area below. There's also a number of options available for changing the appearance of each track (the Options buttons).
[edit] References
- ↑ Valeev T., Yevshin I., Kolpakov F. BioUML Genome Browser. Virtual Biology, 2013, V. 1. doi:10.12704/vb/e8
