Uploaded image for project: 'IGB'
  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

                Descending order - Click to sort in ascending order
                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.
                Hide
                Permalink
                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 -

                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.

                  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: