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  1. UGENE
  2. UGENE-7504

Features are exported (to Fasta) wrongly when complement(join(rangeA,rangeB))

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 41, 40.1
    • Fix Version/s: None
    • Component/s: Basic-Nucl
    • Environment:

      In all environments, I guess (I'm working on Debian GNU/Linux with kernel 5.10.0-7-amd64).

    • Sprint:
      DEV-42-1
    • Affect Type:
      Userdefined

      Description

      When exporting a feature e.g. "complement(join(1427..1636,1641..2423))" into a Fasta sequence, UGENE exports nucleotide sequences that are on the complementary strand (which is okay since we have the "complement" keyword), but in the wrong order of the coding regions: in this case it results into the concatenation of (1) the complement of the nucleotides from position 1636 down to 1427, followed by (2) the complement of the nucleotides from position 2423 down to 1641.

      The above is wrong in terms of the order in which the CDS to be joined are taken into account, as we should get the concatenation of (1) the complement of the nucleotides from position 2423 down to 1641, followed by (2) the complement of the nucleotides from position 1636 down to 1427. Therefore we abide by the strict direction from 5' to 3' on the complementary strand.

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            Assignee:
            yalgaer Yuliya Algaer
            Reporter:
            jbde Jean-Baka Domelevo Entfellner
            Watchers:
            2 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: