3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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20 <head><title>Alignment Quality Annotation</title></head>
22 <p><strong>Alignment Quality Annotation</strong></p>
23 <p>Alignment Quality is one of the automatically calculated
24 quantitative alignment
25 annotations displayed below the columns of a multiple sequence
26 alignment (and can be used to shade the alignment). It is an ad-hoc
27 measure of the likelihood of observing the mutations (if any) in a
28 particular column of the alignment.</p>
30 More precisely, the quality score is inversely proportional to the
31 average cost of all pairs of mutations observed in a particular column
32 of the alignment - a high alignment quality score for a column would
33 suggest that there are no mutations, or most mutations observed are
37 <p><em>The Algorithm</em><br>
38 The quality score is calculated for each column in an alignment by
39 summing, for all mutations, the ratio of the two BLOSUM 62 scores for
40 a mutation pair and each residue's conserved BLOSUM62 score (which
41 is higher). This value is normalised for each column, and then plotted
42 on a scale from 0 to 1.
45 Multiple alignment algorithms using the BLOSUM 62 substition matrices
46 should, in theory, maximise alignment quality for an un-gapped
47 alignment, and locally maximise quality for gapped alignments.