Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-1312

Translation from DNA to Amino Acids fails

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Critical
    • Resolution: Incomplete
    • Affects Version/s: 2.7, 2.8
    • Fix Version/s: 2.8.0b1
    • Component/s: analysis, na, Properties and Preferences
    • Labels:
      None
    • Environment:
      Mac OSX lion
      Macbook Air 2012

      Description

      Trying to translate a nucleotide alignment results in the error:

      "Translation failed. Please select at least three bases in at least one sequence in order to perform a cDNA translation"

      when selecting the entire alignment. Translating only a subset of the columns works in some cases, but not others.

        Attachments

        1. example_align.fasta
          3 kB
          D Sheward
        2. testalign.fasta
          0.1 kB
          D Sheward

          Issue Links

          depends on

          Bug - A problem which impairs or prevents the functions of the product. JAL-1339 Support translation of codons containing ambiguous nucleotides

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-790 Ambiguity codes not supported in PID calculation for trees

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1027 nucleotide substitution matrix that supports rna and ambiguity codes

          • 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-1340 redundancy highlighting is erratic at 0% and 100%

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

          New Feature - A new feature of the product, which has yet to be developed. JAL-1409 cDNA-protein alignment translations include # to indicate codons that align but include frameshifts

          • Major - Major loss of function.
          • Open

          New Feature - A new feature of the product, which has yet to be developed. JAL-1035 support '*' in amino acid sequences to indicate stop codon

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              dsheward D Sheward
              Votes:
              0 Vote for this issue
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: