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  1. Jalview
  2. JAL-2397

Correct PCA (Jalview/SeqSpace) and substitution matrix based tree treatment of gap scores

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    Details

    • Type: Task
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.1
    • Fix Version/s: 2.10.2
    • Component/s: analysis
    • Labels:
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      Description

      Tree distances calculation uses column 23 of the Blosum62 matrix to score char-gap (as -4) or gap-gap (as +1).
      PCA calculation uses column 22 (residue 'X') which scores 0 for A/S/T and -1 or -2 for other residues (-1 for X-X).
      a) should these be consistent?
      b) should they both use zero for gap scores?

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          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2500 minor differences in topology for computed trees compared with older versions of Jalview

          • Trivial - Cosmetic problem like misspelt words or misaligned text.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2379 Improve PCA memory management

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-2398 Blosum62 C->R is 3, should be -3

          • Major - Major loss of function.
          • Closed

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Updated:
                Resolved: