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  1. UGENE
  2. UGENE-6459

Ambiguous characters are treated like 'N' in find pattern algorithm when search on the reverse-complement strand is performed

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 1.32
    • Fix Version/s: 33
    • Component/s: Basic-Nucl
    • Labels:
    • Story Points:
      2
    • Tests Type:
      GUI automatic
    • Sprint:
      DEV-33-5, DEV-33-6, DEV-33-7
    • Affect Type:
      Userdefined

      Description

      Scenario:

      1. Open "data/samples/Genbank/murine.gb".
      2. Open "Search in Sequence" options panel tab.
      3. Set "Substitute" algorithm. Check "Search with ambiguous bases" checkbox.
      4. Ensure that the search is performed on both strands (it is the default value).
      5. Enter the following pattern: "YYYGYY".
        Current result: 1725 results are found. The first result is (9..14). It is incorrect.

      It happens because during the search the pattern is modified to it's reverse-complement to search on the reverse-complement strand. This operation is performed incorrectly: ambiguous characters are converted into 'N' instead of corresponding ambiguous character.

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            Assignee:
            kir Kirill Rasputin
            Reporter:
            atiunov Aleksey Tiunov [X] (Inactive)
            Assigned Tester:
            Aleksey Tiunov [X] (Inactive)
            Watchers:
            3 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: