Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-7959

Add "BLAST selected primer pairs" option

    XMLWordPrintable

    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 50
    • Component/s: None
    • Labels:
    • Epic Link:
    • Sprint:
      DEV-49-5, DEV-49-RELEASE, DEV-50-1
    • Affect Type:
      Userdefined

      Description

      In the NCBI/local BLAST dialogs, you need to add a checkbox "BLAST selected primer pairs", which should appear (and be checked by default) only if primers/parent groups of primers that were found using Primer3 are selected (at least one pair of primers from the same group ). We define the menu item “Create PCR Product...” in a same way, if you want to see how this is done there.

      Run BLAST for each primer pair. One primer - one BLAST. Only the results that both primers have are shown (check by accession number) and are marked with a pair of joined annotations adjacent to the primers (ATTENTION: if possible, run one blast per pair of primers, I’m not sure if this is possible or easy) .

      Need to edit qualifiers. Either one qualifier contains information for both primers (if it can be combined), or save both qualifiers with postfixes like _forward and _reverse

        Attachments

        1. image-2023-12-25-15-25-08-864.png
          image-2023-12-25-15-25-08-864.png
          77 kB
        2. screenshot-1.png
          screenshot-1.png
          104 kB
        3. screenshot-2.png
          screenshot-2.png
          45 kB
        4. screenshot-3.png
          screenshot-3.png
          46 kB
        5. screenshot-4.png
          screenshot-4.png
          77 kB
        6. screenshot-5.png
          screenshot-5.png
          11 kB

          Issue Links

            Activity

              People

              Assignee:
              dsukhomlinov Dmitrii Sukhomlinov
              Reporter:
              dsukhomlinov Dmitrii Sukhomlinov
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: