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  1. Jalview
  2. JAL-2640

Enhance Ensembl ID fetcher to retrieve specific peptide when multiple peptide products exist for resolved locus

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    • Type: Task
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
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      Description

      Followon from JAL-2582:

      When using 'fetch database references' to add refs & annotation, ensembl peptide IDs that resolve to shorter or truncated isoforms of a gene receive cross-references to longer isoforms that are spliced the same way. Probably need to include logic in the Ensembl sequence fetcher that only returns the specifically requested sequence in the alignment to fix this.

      Impact: Jalview currently does more work than is strictly necessary and may create curious CDS cross references when resolving sequences with Ensembl peptide IDs against Ensembl to be able to discover CDS.

      Currrently missing an ID demonstrating the problem.

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Created:
                Updated: