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  1. Jalview
  2. JAL-2198

support extended base-pair annotation in Jalview and linked VARNA view

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.10.5
    • Fix Version/s: None
    • Component/s: na, Structures
    • Labels:
      None

      Description

      Jalview 2.9 and onwards support extended base-pairing annotations (e.g. 'A-Z' pair with 'a-z'..). However these pairs are not yet displayed on the linked VARNA view for a structure. At some point since, Jalview lost the ability to parse extended secondary structure notation from Stockholm.

      - verify what sources of secondary structure data support extended base-pair annotation
      - add support for import in Stockholm
      - add support for viewing/persisting VARNA views based on extended base-pair annotation

        Attachments

          Issue Links

          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-1941 Exception when retrieving RnaView RNA secondary structure

          • Critical - Crashes, loss of data, severe memory leak.
          • In Progress

          Bug - A problem which impairs or prevents the functions of the product. JAL-1863 Cannot export and reimport RNA secondary structure via jalview annotation file

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

          Task - A task that needs to be done. JAL-2187 Test Jalview 2.10 with DockeRNA docker based RNA services

          • Major - Major loss of function.
          • Open

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: