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  1. IGB
  2. IGBF-900

IPS search may fail for some gene models

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          While testing I noticed that the IPS Search may fail for some gene models such as this one from the Bos Taurus genome, Chr1: NM_174504

          After taking a look at this further it seems that this is failing when running through IPS without using IGB.

          This may be because these gene models contain several stop codons in their protein sequence. (See screenshot).

          We should examine why these gene models contain these stop codons.

            Attachments

              Issue Links

              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-906 Add a descriptive message in IPS tab of ProtAnnot for gene models containing no CDS info

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-907 Provide a descriptive message in IPS tab of ProtAnnot for gene models containing multiple stop codons

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                mason Mason Meyer (Inactive) created issue -
                mason Mason Meyer (Inactive) made changes -
                Field Original Value New Value
                Epic Link IGBF-439 [ 15497 ]
                mason Mason Meyer (Inactive) made changes -
                Rank Ranked higher
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                mason Mason Meyer (Inactive) added a comment -

                I think that a failure occurs for any protein sequences that contains more than one stop codon and for gene models that do not have a CDS start or end.

                Show
                mason Mason Meyer (Inactive) added a comment - I think that a failure occurs for any protein sequences that contains more than one stop codon and for gene models that do not have a CDS start or end.
                dcnorris David Norris (Inactive) made changes -
                Rank Ranked lower
                dcnorris David Norris (Inactive) made changes -
                Rank Ranked higher
                dcnorris David Norris (Inactive) made changes -
                Sprint Backlog Grooming Meeting [ 34 ] Backlog Grooming Meeting 2 [ 35 ]
                mason Mason Meyer (Inactive) made changes -
                Link This issue relates to IGBF-906 [ IGBF-906 ]
                mason Mason Meyer (Inactive) made changes -
                Link This issue relates to IGBF-907 [ IGBF-907 ]
                Hide
                Permalink
                mason Mason Meyer (Inactive) added a comment -

                This story has been separated into 2 stories: IGBF-906 and IGBF-907.

                Since this story is no longer needed it will now be closed.

                Show
                mason Mason Meyer (Inactive) added a comment - This story has been separated into 2 stories: IGBF-906 and IGBF-907 . Since this story is no longer needed it will now be closed.
                mason Mason Meyer (Inactive) made changes -
                Assignee Mason Meyer [ mason ]
                mason Mason Meyer (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Open [ 1 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 16310 ] Fall 2019 Workflow Update [ 19632 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19632 ] Revised Fall 2019 Workflow Update [ 21751 ]

                  People

                  • Assignee:
                    mason Mason Meyer (Inactive)
                    Reporter:
                    mason Mason Meyer (Inactive)
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: