Alignment Quality Annotation
-Alignment Quality is one of the automatically calculated -quantitative alignment -annotations displayed below the columns of a multiple sequence -alignment (and can be used to shade the alignment). It is an ad-hoc -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 -of the alignment - a high alignment quality score for a column would -suggest that there are no mutations, or most mutations observed are -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
-on a scale from 0 to 1.
-
-Multiple alignment algorithms using the BLOSUM 62 substition matrices -should, in theory, maximise alignment quality for an un-gapped -alignment, and locally maximise quality for gapped alignments. -
- - + + +Alignment Quality Annotation
+Alignment Quality is one of the automatically calculated +quantitative alignment +annotations displayed below the columns of a multiple sequence +alignment (and can be used to shade the alignment). It is an ad-hoc +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 +of the alignment - a high alignment quality score for a column would +suggest that there are no mutations, or most mutations observed are +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
+on a scale from 0 to 1.
+
+Multiple alignment algorithms using the BLOSUM 62 substition matrices +should, in theory, maximise alignment quality for an un-gapped +alignment, and locally maximise quality for gapped alignments. +
+ +