Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-4913

Values of "Word size", available for "blastp"

    XMLWordPrintable

    Details

    • Story Points:
      2
    • Tests Type:
      GUI automatic
    • Sprint:
      DEV-02/12/2015
    • Affect Type:
      Userdefined

      Description


      The issue must be fixed and tested until Nov. 18!!

      In the original NCBI BLAST online server, the "Word size" parameter can take values "2", "3", and "6". The default value is "6".
      This is not followed in the current UGENE version. There are only values "2" and "3". As a consequence, it is not possible to do BLAST for common sequences, because of timeout.

      Use case:

      1. Open an amino acid sequence (e.g. open 1WC7 and use the sequence of one of the chains).
      2. Select the whole sequence.
      3. Open the NCBI BLAST dialog.
        Expected result: the "blastp" tool is set up.
      4. Open the "Advanced options" tab.
        Expected result: The "Word size" parameter is set to "6".
      5. Start the search.
        Expected result: The search is finished successfully.

        Attachments

          Activity

            People

            Assignee:
            dkandrov Denis Kandrov
            Reporter:
            oigl Olga Golosova
            Assigned Tester:
            Aleksey Tiunov [X] (Inactive)
            Watchers:
            2 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: