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  1. Jalview
  2. JAL-2862

Jalview does not import reverse-strand RNA sequences via Stockholm

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: file format issue, na
    • Labels:

      Description

      Import of sequences via stockholm where the end is lower than the start results in Jalview rewriting the sequence limits as start->end as it is shown in the viewer.

      Import:
      # STOCKHOLM 1.0
      #=GF AC RF00005
      #=GF SQ 3
      #=GF WK Transfer_RNA
      X05914.1/238-170 AAAAAGAU-A-AGCUAA----CU----AAGCUA-C-UGGGU-UCAUACCCCA-UUU------------------------A---UAAA-GGU-UUU-AA--UCCUU-U-UCUUUUU-A
      X05914.1/238-306 UAUAUUUU-G-GUGUAC----GA----UGCACA-A-AAGUU-UUUGAUACUU-UUA------------------------G---UAAU-AGU-UUA-AU--UCUAU-U-AAAUAUA-A
      X05914.1/400-337 AAUGAAUU-G-CCUGAUA---------AAAGGG-U-UAUCU-UGAUAGGGUA-AAU------------------------UA--UGUA-G---GAU-U-----CUA-C-AUUCAUU-G
      //

      Results in three sequences with these IDs:
      # STOCKHOLM 1.0
      X05914.1/238-306 AAAAAGAU-A-AGCUAA----CU----AAGCUA-C-UGGGU-UCAUACCCCA-UUU------------------------A---UAAA-GGU-UUU-AA--UCCUU-U-UCUUUUU-A
      X05914.1/238-306 UAUAUUUU-G-GUGUAC----GA----UGCACA-A-AAGUU-UUUGAUACUU-UUA------------------------G---UAAU-AGU-UUA-AU--UCUAU-U-AAAUAUA-A
      X05914.1/400-463 AAUGAAUU-G-CCUGAUA---------AAAGGG-U-UAUCU-UGAUAGGGUA-AAU------------------------UA--UGUA-G---GAU-U-----CUA-C-AUUCAUU-G
      //

      Import via other formats (e.g. PFAM, by removing stockholm header) results in sequence IDs like:
      X05914.1/238-170/1-69 ...

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              Assignee:
              jprocter Jim Procter
              Reporter:
              jprocter Jim Procter
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                Dates

                Created:
                Updated: