X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fquality.html;h=6f5f000e18d460e762fb7f27c0866657c15cb8d4;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=4846acc3f46316f32dbf7d69ee5b643beb5661bc;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html index 4846acc..6f5f000 100755 --- a/help/html/calculations/quality.html +++ b/help/html/calculations/quality.html @@ -1,20 +1,21 @@ Alignment Quality Annotation @@ -27,7 +28,7 @@ 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 +37,8 @@ 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.