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  1. IGB
  2. IGBF-907

Provide a descriptive message in IPS tab of ProtAnnot for gene models containing multiple stop codons

        Details

        • Type: Improvement
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Sprint:
          Sprint 26

          Description

          Some gene models in IGB may contain multiple stop codons. These gene models will not fail when attempting to run an IPS search on them in ProtAnnot.

          Instead of marking the gene model's IPS status as "Failure" in the IPS tab we should include something more descriptive to show the user that it is not a limitation of ProtAnnot, but instead a limitation of IPS.

          Maybe something like, "Not valid: Translation contains multiple stop codons."

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-900 IPS search may fail for some gene models

              • Major - Major loss of function.
              • Closed

              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

                Activity

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                mason Mason Meyer (Inactive) created issue -
                mason Mason Meyer (Inactive) made changes -
                Field Original Value New Value
                Link This issue relates to IGBF-900 [ IGBF-900 ]
                mason Mason Meyer (Inactive) made changes -
                Link This issue relates to IGBF-906 [ IGBF-906 ]
                mason Mason Meyer (Inactive) made changes -
                Attachment NM_174504 Stop Codons.PNG [ 13168 ]
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                mason Mason Meyer (Inactive) added a comment -

                Discuss other types of validation of gene models before sending to IPS and add error handling.

                Show
                mason Mason Meyer (Inactive) added a comment - Discuss other types of validation of gene models before sending to IPS and add error handling.
                jeckstein John Eckstein (Inactive) made changes -
                Labels ProtAnnot
                jeckstein John Eckstein (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                jeckstein John Eckstein (Inactive) made changes -
                Status In Progress [ 3 ] Needs Testing [ 10002 ]
                jeckstein John Eckstein (Inactive) made changes -
                Assignee John Eckstein [ jeckstein ] Mason Meyer [ mason ]
                mason Mason Meyer (Inactive) made changes -
                Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
                mason Mason Meyer (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Testing In Progress [ 10003 ] Closed [ 6 ]
                mason Mason Meyer (Inactive) made changes -
                Status Closed [ 6 ] Closed [ 6 ]
                mason Mason Meyer (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] Testing In Progress [ 10003 ]
                mason Mason Meyer (Inactive) made changes -
                Comment [ Testing for this issue included:

                -Running IPS on gene models with no CDS start/end to verify that the status field says, "Invalid Protein Sequence: No translation information for this gene model".

                -Running IPS on gene models that do have a CDS start/end to verify that the status message has not change from what is expected.

                Since this issue is resolved it will now be closed. ]
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                mason Mason Meyer (Inactive) added a comment -

                The gene seen in the screenshot above (NM_174504) is from the Bos taurus genome.

                Show
                mason Mason Meyer (Inactive) added a comment - The gene seen in the screenshot above (NM_174504) is from the Bos taurus genome.
                Hide
                Permalink
                mason Mason Meyer (Inactive) added a comment -

                Testing for this issue included:

                -Verifying that genes with no stop codons contain an IPS status message saying, " Invalid Protein Sequence: Translation contains multiple stop codons".

                -Verifying that gene models with stop codons are not affected my this new change.

                Since this issue is resolved it will now be closed.

                Show
                mason Mason Meyer (Inactive) added a comment - Testing for this issue included: -Verifying that genes with no stop codons contain an IPS status message saying, " Invalid Protein Sequence: Translation contains multiple stop codons". -Verifying that gene models with stop codons are not affected my this new change. Since this issue is resolved it will now be closed.
                mason Mason Meyer (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 16318 ] Fall 2019 Workflow Update [ 19637 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19637 ] Revised Fall 2019 Workflow Update [ 21756 ]

                  People

                  • Assignee:
                    mason Mason Meyer (Inactive)
                    Reporter:
                    mason Mason Meyer (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: