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  1. Jalview
  2. JAL-3200

Improve scalability of large RNA alignments

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    Details

    • Type: Task
    • Status: In Progress
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.10.5
    • Fix Version/s: None
    • Component/s: jvdesktop

      Description

      If RF00031_folded.stk sequences are duplicated to an alignment of 1000 sequences:
      - the file is very slow to load
      - there are cpu bottlenecks while loading
      - loading fails with OutOfMemoryError (with 4GB allocated to JVM)
      Investigate for potential performance improvements.
      Lower priority until Jalview raises priority of RNA handling.

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          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-98 conservation / consensus out of memory

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

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated: