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  1. UGENE
  2. UGENE-7918

Create new Primer3 dialog "Presets" feature and add a new preset called RPA (Recombinase polymerase amplification)

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 49
    • Component/s: None
    • Labels:
    • Epic Link:
    • Sprint:
      DEV-49-2, DEV-49-3, DEV-49-4
    • Affect Type:
      Userdefined

      Description

      If you go to the Primer3PlusĀ  website, you will find out, that Primer3Plus has a setting (which in not related to the calculation process itself) called "Load server settings". This parameter has a bunch of different options. Each option sets Primer3 start parameters to settings, which are related to some certain PCR type.

      It is required to create something simular in our Primer3 dialog. This feature will be called "Presets".

      Primer3Plus has this thing on the first page. As far as the Primer3 dialog's first page is already overloaded and it won't be good to split parameters on the first page (they all are connected logically, in some way), it would be better to add a button in the bottom of the dialog called "Presets" (between "Close" and "Save setting").

      Clicking on this button opens a dialog with the same name "Presets".

      This dialog should have a combo box with two states: Default and RPA.

      When you click on the default state, all options are set to the same parameters as now (curret parameters preset is default one).

      The "RPA" preset should set the following parameter:

      • Temperature 20-80 (optimum 55).
      • Primer size 30-35 (optimum 33).
      • Product size 200-500.

      Also RPA should have group box (enabled by default) called "Check complementary" with two options:

      • Max complement pairs - from 1 to inf (4 bp by default).
      • Max G/C pairs - from 0 to 100 % (50% by default).

      If "Check complementary" is checked, we additionlly check result primers for self-/heterodymers. If primers are complemented themself/each other more than by 4 bases, they alre filtered. If they are complemented by 4 or less bases, but more than 50% of complementet pairs are G/C's, primer pair is filterd too.

      Important: save preset state when you switch another preset on

      Show in the result notification information about filered pairs and whi it's been filtered (show self/heterodymers).

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              Assignee:
              dsukhomlinov Dmitrii Sukhomlinov
              Reporter:
              dsukhomlinov Dmitrii Sukhomlinov
              Assigned Tester:
              Svetlana Samoilenko
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                Dates

                Created:
                Updated:
                Resolved: