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  1. Jalview
  2. JAL-3860

propagate mouseover, region highlights and selection events on reference to transcripts and products

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    Details

    • Type: New Feature
    • Status: Open
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2
    • Fix Version/s: None
    • Component/s: cds/protein, Datamodel, genomes
    • Labels:
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      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.

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              Assignee:
              soares Ben Soares
              Reporter:
              jprocter Jim Procter
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                Created:
                Updated: