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  1. UGENE
  2. UGENE-3423

UGENE does not handle annotations joined on different strands

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Won't Fix
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Basic-Nucl
    • Labels:
    • Affect Type:
      Userdefined

      Description

      An internal structure of UGENE sequence annotations does not allow parts of a joined annotation to be located on different strands. UGENE's Genbank format parser also does not handle such annotation locations as "join(1..5, complement(6..8))". Such behavior leads to inablility of the Find Repeats algorithm to search for inverted repeats. Currently, instead of the repeat element located on a complementary strand the algorithm gives the annotation with the same location, but on a direct strand.
      Thus, it is required to add the support of different strands for regions of joined annotations, then change appropriately UGENE format parsers so that they could handle such data and, finally, make all the algorithms producing annotations use this extension.

      The issue relates to UGENE-3134 which is a user request.

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              Assignee:
              yalgaer Yuliya Algaer
              Reporter:
              iprotsyuk Ivan Protsyuk
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                Created:
                Updated:
                Resolved: