X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fquality.html;h=60d67c2372151e142157fc272ea5a9e64ed77afa;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=33507339ed6a0ab958cbf5809dfbc97f7c6f37b1;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html index 3350733..60d67c2 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.