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  1. UGENE
  2. UGENE-8049

error in annotating circular on GenBank LOCUS line

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    Details

    • Type: Bug
    • Status: Tested
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 49
    • Fix Version/s: 50
    • Component/s: Basic-Nucl
    • Labels:
    • Environment:

      RHEL 8 Linux

    • Tests Type:
      Manual scenario
    • Sprint:
      DEV-50-RELEASE
    • Affect Type:
      Userdefined

      Description

      In v49.1, LOCUS lines created by Ugene omit a field indicating the type of molecule (eg. DNA, mRNA, rRNA etc.) This causes some programs to incorrectly read a Ugene-generated circular sequence as linear. The NCBI GenBank release notes prescribe the following format for a LOCUS line:

      LOCUS       CP032762             5868661 bp    DNA     circular BCT 15-OCT-2018
      ------------+--------------+-+---------+---------+---------+---------+---------
      1          13             28 30       40        50        60        70       79
      

       I created a construct and saved in GenBank format:

       LOCUS       pBS_SK-GUS              5978 bp     circular            27-FEB-2024
      

       This file will be read incorrectly as a linear sequence by programs that look for the word circular in field 6, or in column 56. It would be parsed correctly by programs that search for 'circular' anywhere on the LOCUS line. The line can be fixed manually: 

      LOCUS       pBS_SK-GUS              5978 bp    DNA     circular     27-FEB-2024
      

      In previous versions of Ugene (eg. 29) the molecule type field was written. I recommend revising Ugene to explicitly write LOCUS lines in the specific columns described in the NCBI documentation at
      https://ftp.ncbi.nlm.nih.gov/genbank/gbrel.txt

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              Assignee:
              yalgaer Yuliya Algaer
              Reporter:
              frist Dr. Brian Fristensky
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
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                Dates

                Created:
                Updated:
                Resolved: