Bioinformatics.org
[OMICtools]
Not logged in
  • Log in
  • Bioinformatics.org
    Membership (40944+) Group hosting [?] Wiki
    Franklin Award
    Sponsorships

    Careers
    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    Research
    All information groups
    Online databases Online analysis tools Online education tools More tools

    Development
    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    Forums
    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1159 ] GetInfo says 'linear' for circular GenBank files
    Date:
    10/13/11 22:57
    Submitted by:
    B_Fristensky
    Assigned to:
    Alvare
    Category:
    bioLegato
    Priority:
    3
    Ticket group:
    Bug
    Resolution:
    Resolved
    Summary:
    GetInfo says 'linear' for circular GenBank files
    Original submission:
    From the sequence tutorial, use File --> Open to read in X52331.gen. The GenBank file specifies on the LOCUS line
    that this is a circular sequence.

    Once the sequence has been read in, GetInfo shows that the sequence is Linear. Interestingly, if you run DNARNA --> BACHREST on this sequence, the output shows up as being
    Circular. So somehow, the topology information is retained internally within bioLegato, but the Topology is not displayed correctly.

    One further observation: If I change the Toplogy to Circular within GetInfo, the BACHREST output says 'Circular'. If I then change it to 'Linear', the BACHREST output now says
    'Linear'. So the problem seems to be that bioLegato is forgetting to set this menu when the sequence is first read in.



    Please log in to add comments and receive followups via email.
    No followups have been posted
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Open 10/18/11 10:42 Alvare
    resolution_id Not Resolved 10/18/11 10:42 Alvare
    close_date 12/31/69 19:00 10/18/11 10:42 Alvare
    status_id Pending 10/13/11 22:57 B_Fristensky
    priority 5 10/13/11 22:57 B_Fristensky
    assigned_to unset 10/13/11 22:57 B_Fristensky
    resolution_id Unset 10/13/11 22:57 B_Fristensky

     

    Copyright © 2019 · Scilico, LLC