Deprecated! please use https://github.com/VEuPathDB/JBrowse

CanvasSubtracks (View)

Tested with JBrowse 1.16.3

Example Track Configuration:

• geneGroupAttributeName: An attribute of the features which indicates the group. Features with the same value for this attribute will be connected with shading.
• subtracks: list which contains "featureFilters" and "metadata" objects. featureFilters are used to assign features into subtracks and "metadata" is used for configuration/subtrack selection.

{
 ....
    "type": "CanvasSubtracks/View/Track/Synteny"
    "geneGroupAttributeName": "orthomcl_name",
    "subtracks": [
        {
            "featureFilters": {
                "SynType": "gene",
                "Taxon": "Plasmodium falciparum 3D7"
            },
            "label": "pfal3D7 gene",
            "metadata": {
                "Class": "Aconoidasida",
                "Genus": "Plasmodium",
                "Kingdom": "N/A",
                "Phylum": "Apicomplexa",
                "Species": "Plasmodium falciparum"
            },
            "visible": true
        },
        {
            "featureFilters": {
                "SynType": "span",
                "Taxon": "Plasmodium falciparum 3D7"
            },
            "label": "pfal3D7 span",
            "metadata": {
                "Class": "Aconoidasida",
                "Genus": "Plasmodium",
                "Kingdom": "N/A",
                "Phylum": "Apicomplexa",
                "Species": "Plasmodium falciparum"
            },
            "visible": true
        }, 
	....
    ]
}

For Canvas Subtracks without Synteny Shading simply remove the geneGroupAttributeName and change the type to "CanvasSubtracks/View/Track/CanvasSubtracks"

Store

Tested with REST, GFF, NCList which should work fine if you are displaying static alignments.

This plugin provides "CanvasFeatures/Store/SeqFeature/REST" which will add 2 query params to the service call (visibleRegionStart and visibleRegionEnd). This allows the service to do whatever scaling is appropriate for the syntenic region.

data workflow in a nutshell

Most of the heavy lifting is done upstream of this plugin. One possible approach is:

1. Perform all possible pairwise comparisons of genomes and determine all large regions of synteny (we use mercator and MAVID)

2. For each syntenic region, determine the coordinate pairs for each syntenic gene's start to the corresponding gene start in the reference.

3. Create a REST endpoint which when given an arbitrary region (visibleRegionStart->visibleRegionEnd) can get the min and max coord pair for the region and scale the syntenic locations so they can be shown in reference coordinates.

Funding

This plugin was made possible by funding provided by the NIH:National Institute of Allergy and Infectious Diseases (NIAID) to the EuPathDB Bioinformatics Resource Center (BRC).