X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fquality.html;h=6d02b4fa47e8ea8c309426ca6a97a98610244f84;hb=c4b3f11eeec8b3d01027d251054b8390ed4deae2;hp=dae2a2e36d44a6b649e266996c2588d771879d13;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html index dae2a2e..6d02b4f 100755 --- a/help/html/calculations/quality.html +++ b/help/html/calculations/quality.html @@ -1,21 +1,21 @@ +-->
Alignment Quality Annotation
@@ -27,7 +27,7 @@ measure of the likelihood of observing the mutations (if any) in a particular column of the alignment.More precisely, the quality score is inversely proportional to the -average cost of all pairs of mutations oberved in a particular column +average cost of all pairs of mutations observed in a particular column of the alignment - a high alignment quality score for a column would suggest that there are no mutations, or most mutations observed are favourable. @@ -36,8 +36,8 @@ favourable.
The Algorithm
The quality score is calculated for each column in an alignment by
summing, for all mutations, the ratio of the two BLOSUM 62 scores for
-a mutation pair and each residue's conservered BLOSUM62 score (which
-is higher). This valueis normalised for each column, and then plotted
+a mutation pair and each residue's conserved BLOSUM62 score (which
+is higher). This value is normalised for each column, and then plotted
on a scale from 0 to 1.