Hello Brendan.
On 24/05/2012 10:14, Palmer, Brendan wrote:
Could someone provide me with a clearer understanding as to why the
conservation index values go to 9 and are then + or * above this? I
presume * is 100% conserved, but what about +?
OK - I guess by clearer, you mean clearer than this page:
http://www.jalview.org/help/html/calculations/conservation.html
The conservation measure counts the number of amino acid properties
conserved in a column - when all 10 properties are conserved, the
measure would be 10, but then its useful to reflect whether the column
contains a conserved residue, or one or more substitutions between
residues with the same physicochemical property. Because we wanted a
per-column symbol, we use '*' to mean the column is conserved (ie
conservation==11), and '+' to means the column contains residues with
the same physicochemical properties (conservation == 10).
Hope that clears up any confusion - I'll amend the built in
documentation to explicitly mention the */+ convention.
Jim.
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