Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-6814

Primer3 and "product size range" that equals to the sequence length

    XMLWordPrintable

    Details

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

      Description

      There is difference in behavior between the command-line Primer3 version (https://github.com/primer3-org/primer3) and the version, integrated into UGENE. The latter one looks strange. More specifically, when the "Product size ranges" parameter in the Primer3 dialog is set to the length of the sequence ("seq_length-seq_length"), some result primers are partially located on both the beginning and the end of the sequence, even when the input sequence is NOT circular!

      Scenario:

      1. Open "IL2_human.fasta".
        Expected result: the sequence length is 402 bp.
      2. Open the Primer3 dialog.
      3. Set "Product size ranges" to "402-402".
      4. Click "Pick primers".
        Expected result: when I run command-line Primer3 it returns NO results in this case. So, probably, there should be no result in UGENE as well.
        Current result: five pairs are found. Some pairs contains primers with coordinates "complement(402..402,1..23)". BUT the sequence is NOT circular.

      To check this in the command line use the attached "input" file.

      ./primer3_core .../input
      

        Attachments

        1. IL2_human.fasta
          0.4 kB
          Olga Golosova
        2. input
          0.6 kB
          Olga Golosova

          Activity

            People

            Assignee:
            dsukhomlinov Dmitrii Sukhomlinov
            Reporter:
            oigl Olga Golosova
            Watchers:
            2 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: