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  1. Jalview
  2. JAL-1409

cDNA-protein alignment translations include # to indicate codons that align but include frameshifts

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    Details

    • Type: New Feature
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
    • Labels:
      None

      Description

      Situations where the optimal nucleotide alignment of a codon include gaps like:

      >a
      1-23-
      >b
      -12-3

      Could be represented as:
      >tr_a
      #X#
      >tr_b
      #X#

      to indicate that the second position aligns perfectly, but position 1 and three are misaligned.

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          Issue Links

          related with

          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

          New Feature - A new feature of the product, which has yet to be developed. JAL-845 Allow DNA and protein alignments to be linked so one follows the other

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: