Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-1027

nucleotide substitution matrix that supports rna and ambiguity codes

    XMLWordPrintable

    Details

    • Type: Improvement
    • Status: Resolved
    • Priority: Minor
    • Resolution: Incomplete
    • Affects Version/s: 2.8, 2.8.0b1
    • Fix Version/s: 2.8, 2.8.0b1
    • Component/s: analysis, na
    • Labels:
      None

      Description

      The nucleotide substitution matrix in jalview.schemes.ResidueProperties should properly reflect different ambiguity equivalences, e.g. purine vs pyrimidine vs any unknown nucleotide, and T==U for rna/dna translation.

        Attachments

          Issue Links

          blocks

          Bug - A problem which impairs or prevents the functions of the product. JAL-1013 PCA analysis of RNA or DNA uses blosum62 matrix in calculation

          • Major - Major loss of function.
          • Resolved
          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-1167 documentation for score matrices used in Jalview

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-1312 Translation from DNA to Amino Acids fails

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

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
              Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: