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  1. UGENE
  2. UGENE-6276

Results of "blastx" are always located on the direct strand

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 1.31.1
    • Fix Version/s: 33
    • Component/s: Basic-Nucl
    • Labels:
    • Story Points:
      2
    • Sprint:
      DEV-33-1, DEV-33-2
    • Affect Type:
      Userdefined

      Description

      Precondition:

      • There is a nucleotide sequence (e.g. "murine.fa").
      • There is a BLAST+ database with amino acid sequences homologous to the translated nucleotide sequence (e.g. unpacked "murinedb2" - note that it was built from amino acid translation of "murine" reverse-complement sequence).

      Scenario:

      1. Open the nucleotide sequence.
      2. Select "Actions > Analyze > Query with local BLAST+".
      3. In the appeared dialog set "Select search" to "blastx", specify the database, click "Search".
        Expected result: "blast result" annotation, located in region 2..5833, is located on the reverse-complement strand.
        Current result: all "blast result" annotations are located on the direct strand.

      For details, see the attached "murine.xml" file also. The original BLAST tool return an xml file. For the annotation specified above in the "Expected result", "Hsp_query-frame" is negative ("-1"). Currently, this is not taken into account.

      See http://ugene.net/forum/YaBB.pl?num=1531453404/5#5.

        Attachments

        1. murinedb2.zip
          2 kB
        2. murine.fa
          6 kB
        3. murine.xml
          13 kB

          Activity

            People

            Assignee:
            kir Kirill Rasputin
            Reporter:
            oigl Olga Golosova
            Assigned Tester:
            Dmitrii Sukhomlinov
            Watchers:
            1 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: