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  1. UGENE
  2. UGENE-6641

Exclude "X" character from extended DNA and RNA alphabets

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Won't Fix
    • Affects Version/s: 33
    • Fix Version/s: None
    • Component/s: General
    • Labels:
      None
    • Affect Type:
      Userdefined

      Description

      For some reason character "X" is currently included into extended DNA and RNA alphabets in UGENE, see BaseAlphabets.cpp:

          //extended NUCL DNA
          {...
              fill(map, "ACGTMRWSYKVHDBNX-", Qt::CaseInsensitive); //X == N
            ...}
      
          //extended NUCL RNA
          {...
              fill(map, "ACGUMRWSYKVHDBNX-", Qt::CaseInsensitive); //X == N
           ...}
      

      "X" is not included into the standard degenerate base symbols, see e. g. https://en.wikipedia.org/wiki/Nucleic_acid_notation#cite_note-iupac-2.

      Note that "X" might be used sometimes for denoting a xeno nucleic acid.
      However, the character shouldn't be included into the "Extended DNA alphabet" or "Extended RNA alphabet" in UGENE. Some tools, available for these alphabets, may be not designed to process sequences with "X" character.

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            Assignee:
            Unassigned
            Reporter:
            oigl Olga Golosova
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              Created:
              Updated:
              Resolved: