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  1. Jalview
  2. JAL-2301

Threonine (T) is reported as !hydrophobic in Conservation, should be hydrophobic

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.0
    • Fix Version/s: 2.10.1
    • Component/s: jvdesktop, jvlite
    • Labels:
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      Description

      In ResidueProperties static initialisation:
          hydrophobic.put("T",Integer.valueOf(0)); // 0 == residue lacks property
      - has been that way (or new Integer(0)) for at least 10 years

      This is contrary to the Venn diagram and matrix for the conservation calculation description.

      See for example uniref50.fa column 68 which is all T, reported as !hydrophobic in the conservation annotation tooltip.

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