UGENE
  1. UGENE
  2. UGENE-6136

Problem finding a primer when characters insertion is required at the beginning of the primer

    Details

    • Type: Bug Bug
    • Status: Closed Closed
    • Priority: Blocker Blocker
    • Resolution: Fixed
    • Affects Version/s: 1.30
    • Fix Version/s: 1.31
    • Component/s: Basic-Nucl
    • Labels:
    • Story Points:
      3
    • Sprint:
      DEV-31-4, DEV-31-5, DEV-31-6-RELEASE
    • Affect Type:
      Userdefined

      Description

      See the attached archive. There are two sequences and one file with forward and reverse primers. The second (extended) sequence has additional 12 'T' characters at the beggining.

      Scenario:

      1. Open a sequence.
      2. Open the "In Silico PCR" tab on the options panel.
      3. Input the forward and reverse primers from the third file.
      4. Set the number of mismatches for the forward primer to "27" (note that it is enough to set the value to "22" for the extended sequence).
      5. Click "Find product(s) anyway".
        Current result: A product is found only in case of the extended sequence.
        Expected result: The product is found in both cases.

      In the attached pictures you can see that in case of "not_extended" sequence the primers searching algorithm needs to insert additional gaps at the beginning of the sequence, but it doesn't do that. In case of "extended" sequence, the beginning is already filled with 'T' chars, so the algorithm can find the place correctly.

      This issue was created according the following issue on GitHub:
      https://github.com/ugeneunipro/ugene/issues/38

      1. ugene_sequences.tar.gz
        1 kB
        Dmitrii Sukhomlinov
      1. extended.png
        14 kB
      2. not_extended.png
        13 kB

        Activity

        Hide
        Dmitrii Sukhomlinov
        added a comment - - edited

        Previously, the number of mismatches was calculated as a minimum of values:

        • "Mismatches", specified on the "In Silico PCR" tab of the options panel
        • A half of the primer length

        This has been modified as follows: there may be any number of mismatches, but they are searched for in the 5' part of the primer, i.e. "the primer length - 3' perfect match".

        Show
        Dmitrii Sukhomlinov
        added a comment - - edited Previously, the number of mismatches was calculated as a minimum of values: "Mismatches", specified on the "In Silico PCR" tab of the options panel A half of the primer length This has been modified as follows: there may be any number of mismatches, but they are searched for in the 5' part of the primer, i.e. "the primer length - 3' perfect match".
        Hide
        Aleksey Tiunov
        added a comment -

        Something is wrong.

        Show
        Aleksey Tiunov
        added a comment - Something is wrong.

          People

          • Assignee:
            Dmitrii Sukhomlinov
            Reporter:
            Dmitrii Sukhomlinov
            Assigned Tester:
            Svetlana Samoilenko
          • Votes:
            0 Vote for this issue
            Watchers:
            3 Start watching this issue

            Dates

            • Created:
              Updated:
              Resolved:

              Agile