While genome annotation is generally provided by the Ensembl project, the genome browser is also extensible to show annotation of custom data sets. External data sets can be integrated in several ways differing in flexibility, efficiency and data persistence.
You may also share your data source with others if you wish to do so.
Ensembl offers you the ability to display your own data sets in:
Ensembl provides a simple, form-based upload function to store small custom data sets directly in the genome browser.
For species with assembled chromosomes, Ensembl KaryoView can be configured to display a series of user-defined data points either along a single chromosome ideogram, such as those displayed on Ensembl MapView, or along an entire karyotype ideogram. Visualising sets of genomic data with discrete positions can be extremely useful to get an overview of your data distribution and to identify any hot or cold spots that might not be immediately obvious.
Ensembl KaryoView displays are accessible via the "Map your data onto this chromosome" option in the left-hand navigation column on Ensembl MapView pages. MapView displays in turn are accessible by clicking a chromosome on an Ensembl species entry page.
KaryoView can be configured to display the data set as a variety of boxes, lines and arrows against the chromosomes. If desired, you can change the chromosome when you configure KaryoView. More information about the supported data set formats and display configuration would be available from the KaryoView help document.
To annotate features along the genome sequence like Ensembl does on ContigView and CytoView, open the 'DAS Sources' menu on these displays. The 'Manage sources' option will lead to a DasConfView web form. Select 'Upload your data' to start the upload dialogue.
Custom data sets are generally specified as a list of features, where each line is a tab-delimited record of chromosome number, start base, end base and feature name values. More detailed specification of the supported upload format would be available from the DasConfView help document.
These work much the same way as file uploads - see section above.
The addition of URL-based data sets provides a very simple means to add rather small custom data sets to the Ensembl genome browser. As Ensembl needs reading the data set before it can include annotation into its displays, the data set must be placed on a web server publicly accessible via the internet. The data is private in the sense that Ensembl does not advertise the URL to other users and as permanent as you provide it on your web server. You may eventually want to inform your collaborators about the URL.
The URL-based data format is compatible with the UCSC Custom Track format, so that the same file can be used for both the UCSC genome browser and the Ensembl genome browser.
Once stored on a web server, the external data set can be added via the 'DAS Sources' menu on ContigView and CytoView pages. Follow the 'URL-based data' option in the menu to specify the URL.
More information about the data format is available from the URL-based data help document.
The Distributed Annotation System (DAS) is a protocol for providing genome, gene and protein annotations over the internet. A DAS client can connect to several annotation servers simultaneously, allowing users to see and compare annotations from different sources.
Ensembl provides a list of pre-configured DAS sources in the 'DAS Sources' menus of ContigView and CytoView displays, which annotate features on a genome sequence assembly. While these sources can simply be activated from the menu, DAS sources provided by other servers can be added via the 'Manage sources' option.
Ensembl GeneView, TransView and ProtView displays provide specific information about genes, transcripts and their translations, if any, respectively. A 'DAS Sources' section on all those displays contains a list of pre-configured Distributed Annotation System (DAS) sources that extend the information stored in Ensembl. Additional data sources, as well as external DAS servers can be attached via the 'Manage sources' button.
Following the 'Manage sources' option will lead to the Ensembl DasConfView display. Several DAS servers serving annotation sources are available from the DAS Registry. Other servers could be added by providing a URL via the 'Add Data Sources' option in the left-hand navigation column.
More information about DAS source attachment and configuration would be available from the DasConfView help document.
DAS is widely used by Ensembl to include external annotations on its ContigView, CytoView, GeneView, TransView and ProtView displays. Ensembl also has its own Ensembl-DAS reference server. More...
© 2024 Inserm. Hosted by genouest.org. This product includes software developed by Ensembl.
