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  1. Jalview
  2. JAL-1705

Ensembl sequence fetching

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.9, 2.10.0
    • Fix Version/s: 2.10.0
    • Component/s: data retrieval services
    • Labels:
      None

      Description

      Ids for ENSEMBL should be resolvable as annotated sequences via the sequence fetcher.

      Some relevant snippets re the REST api over at biostars:
      https://www.biostars.org/p/137514/#137540

      Key milestones (please enhance and improve, and add additional features here!):
      0. Retrieve sequence for full ID
      1. Parse relationships between sequences: ENSP/ENST for protein and transcript
      2. Taxonomy + compara

        Attachments

          Issue Links

          blocks

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2050 Hide introns in locus/transcript view

          • Major - Major loss of function.
          • Closed
          depends on

          Task - A task that needs to be done. JAL-2001 Refactor ColumnSelection to store ranges rather than individual selected columns

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2205 Improve efficiency of datamodel for handling locus datasets

          • Major - Major loss of function.
          • Open
          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-1997 (Optional) tooltip for entries in database tree

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: