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  1. Jalview
  2. JAL-2049

Protein product variant features from genome variant annotation

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.10.0
    • Component/s: analysis
    • Labels:
      None

      Description

      Jalview could automatically detect and annotate positions in protein products which are subject to variation due to observed SNPs and other types of genomic sequence variant annotation. These types of annotation are already provided by ensembl.

      Sites of peptide variation would be shown as sequence features, initially, which are automatically added to cross-referenced protein products. The description gives information about the amino acid variation observed at each site.

      Much of this has already come in under JAL-1705 - this issue is to track specific updates to this capability independently of Ensembl data retrieval.

        Attachments

          Issue Links

          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2230 variants missing on transcript CDS|seq in cDNA/Product view

          • Critical - Crashes, loss of data, severe memory leak.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2041 clinical significance field not preserved in variant annotation from Ensembl

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-326 Structure colouring from disulphide features not localised to cysteines

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          Task - A task that needs to be done. JAL-2628 Review new Uniprot Proteins REST API

          • Major - Major loss of function.
          • In Progress

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2901 Handle calculation of co-occurring variants on protein

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • In Progress

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: