3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>Alignment Quality Annotation</title></head>
21 <p><strong>Alignment Quality Annotation</strong></p>
22 <p>Alignment Quality is one of the automatically calculated
23 quantitative alignment
24 annotations displayed below the columns of a multiple sequence
25 alignment (and can be used to shade the alignment). It is an ad-hoc
26 measure of the likelihood of observing the mutations (if any) in a
27 particular column of the alignment.</p>
29 More precisely, the quality score is inversely proportional to the
30 average cost of all pairs of mutations observed in a particular column
31 of the alignment - a high alignment quality score for a column would
32 suggest that there are no mutations, or most mutations observed are
36 <p><em>The Algorithm</em><br>
37 The quality score is calculated for each column in an alignment by
38 summing, for all mutations, the ratio of the two BLOSUM 62 scores for
39 a mutation pair and each residue's conserved BLOSUM62 score (which
40 is higher). This value is normalised for each column, and then plotted
41 on a scale from 0 to 1.
44 Multiple alignment algorithms using the BLOSUM 62 substition matrices
45 should, in theory, maximise alignment quality for an un-gapped
46 alignment, and locally maximise quality for gapped alignments.