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  1. Jalview
  2. JAL-2685

include start/end position of aligned region in pairwise alignment reports

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.10.3
    • Component/s: analysis
    • Labels:
      None

      Description

      Aligning two sequences like:
      >FER_CAPAN/40-93 Ferredoxin, chloroplast precursor
      NGGKVTCMASYKVKLITPDGPIEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSS
      >FER1_SOLLC/75-111 Ferredoxin-1, chloroplast precursor
      AEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFL

      Yields a report like:
      Score = 1000.0
      Length of alignment = 19
      Sequence FER1_SOLLC : 75 - 111 (Sequence length = 37)
      Sequence FER_CAPAN : 40 - 93 (Sequence length = 54)

      FER1_SOLLC AEEEGHDLPYSCRAGSCSS
                 ||| |||||||||||||||
       FER_CAPAN AEEAGHDLPYSCRAGSCSS

      Percentage ID = 94.74

      But - the report omits the start and end position for the aligned portion of each sequence!

        Attachments

          Issue Links

          blocks

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2703 Propagate hidden columns to Pairwise Alignment outputs

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-2684 pairwise alignment of region selections do not inherit correct start/end position

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              dmamartin dmamartin
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                Dates

                Created:
                Updated:
                Resolved: