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As the Example1 above shows, both sequence strands are queried by default.

To modify this behavior select the Actions ‣ Query Sequence Mode item in the main menu or Query Sequence Mode toolbar button. You can choose between the following values:

  • Direct strand — the search is performed for the direct strand only.

    Note, that the results can still be found in the complement strand if you have set the Any or Backward direction for an element.

  • Reverse complementary strand — the search is performed for the reverse complementary strand.

  • Both strands — the search is performed for the both strands.


Create the following schema:

  1. The Smith-Waterman algorithm element with AAG patern and the Forward direction.
  2. The Smith-Waterman element with CGG pattern and the Forward direction.
  3. Add a constraint to these elements.
  4. Set the Query Sequence Mode to Direct strand.
  5. Run the schema for a sequence.

Only the following results will be found:

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