Details
-
Type: New Feature
-
Status: In Progress
-
Priority: Blocker
-
Resolution: Unresolved
-
Affects Version/s: 2.11.2, 2.11.3, 2.11.4
-
Fix Version/s: 2.11.4
-
Component/s: cds/protein, Datamodel, genomes
-
Labels:None
-
Epic Link:
-
Urgency:Highest
Description
Genome browsers normally send events involving one or more regions on a genome. When Jalview handles these events, it should be able to:
- efficiently identify sequences intersecting with those regions
- translate events (mouse over, selection, highlight) events on those regions to intersecting sequences
-- transcripts derived from ENSG reference sequences
-- CDS
-- Protein products
Right now, there are inconsistencies in the way reference contig associations are handled between different sources of transcript, CDS and protein product sequences. ENA contigs can be imported directly and any CDS/Product relationships visualised via 'show cross references': there, sequence mappings are explicit between CDS and reference contig, and mouse overs on the original contig are propagated. For Ensembl, however, genomic loci are imported as one or more ENSG reference sequences, and any transcripts also imported as primary sequences. CDS/Protein relationships are then made to the transcript, rather than the ENSG reference locus, so mouseovers are not propagated from or to the reference.
A first step would be to provide highlighting of transcripts and products associated with a position on a particular genomic reference sequence as returned by the Ensembl Sequence fetcher.
- efficiently identify sequences intersecting with those regions
- translate events (mouse over, selection, highlight) events on those regions to intersecting sequences
-- transcripts derived from ENSG reference sequences
-- CDS
-- Protein products
Right now, there are inconsistencies in the way reference contig associations are handled between different sources of transcript, CDS and protein product sequences. ENA contigs can be imported directly and any CDS/Product relationships visualised via 'show cross references': there, sequence mappings are explicit between CDS and reference contig, and mouse overs on the original contig are propagated. For Ensembl, however, genomic loci are imported as one or more ENSG reference sequences, and any transcripts also imported as primary sequences. CDS/Protein relationships are then made to the transcript, rather than the ENSG reference locus, so mouseovers are not propagated from or to the reference.
A first step would be to provide highlighting of transcripts and products associated with a position on a particular genomic reference sequence as returned by the Ensembl Sequence fetcher.
Attachments
Issue Links
- depends on
-
JAL-4328 Some ensembl queries may not work reliably in 2.11.3.0, 2.11.4.0
- Closed
-
JAL-3982 Mouseover on genomic loci propagated to 2D and 3D structures of transcripts and products
- Ready for testing
- related with
-
JAL-3851 Jalview REST API for Interoperation with Genome Browsers
- In Progress
- mentioned on
(1 mentioned on)