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  1. Jalview
  2. JAL-2703

Propagate hidden columns to Pairwise Alignment outputs

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: analysis
    • Labels:
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      Description

      If pairwise alignment is performed on a region that includes one or more hidden columns, the hidden columns should ideally be included in the results of the pairwise alignment.

      For example this extract from uniref50.fa:

      >Q93XJ9_SOLTU
      PVVTSL-KAISNV
      >FER1_PEA
      PMPMSV-TTTKAF

      Hide columns 6-9 to leave
      PVVTSISNV
      PMPMSTKAF
      Select these sequences and do Calculate | Pairwise Alignment.
      The resulting output can be viewed as an alignment which is (with no hidden columns)
      PMSTKAF
      PVVTSIS
      (note the algorithm leaves sequence ordering reversed).
      This should correctly show
      1) a hidden column after column 3: PMS^TKAF
          - the hidden positions in FER1_PEA are V-TT
          - Q93XJ9_SOLTU has no hidden positions here (implicit gaps inserted)
      2) a hidden column after column 5: PVVTS^IS
          - the hidden positions in Q93XJ9_SOLTU are L-KA
          - FER1_PEA has no hidden positions here (implicit gaps inserted)

      ...and similarly if there are multiple hidden columns in the aligned sequences!

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              Assignee:
              jprocter Jim Procter
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated: