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.
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19 <head><title>Alignment Conservation Annotation</title></head>
20 <body><p><strong>Alignment Conservation Annotation</strong></p>
21 <p>This is an automatically calculated quantitative alignment
22 annotation which measures the number of conserved physico-chemical
23 properties conserved for each column of the alignment. Its calculation
24 is based on the one used in
25 the AMAS method of multiple sequence alignment analysis :<br>
27 C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
28 for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>
31 <em><a href="http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html">View an HTML version of the paper</a></em>
33 <p>Conservation is measured as a numerical index reflecting the conservation of
34 <a href="../misc/aaproperties.html">physico-chemical
35 properties</a> in the alignment: Identities score highest, and the next most
36 conserved group contain substitutions to amino acids lying in the same physico-chemical
38 <p>Conservation is visualised on the alignment or a sequence group
39 as a histogram giving the score for each column. Conserved columns are
40 indicated by '*' (score of 11 with default amino acid property
41 grouping), and columns with mutations where all properties are
42 conserved are marked with a '+' (score of 10, indicating all
43 properties are conserved).</p>
45 <p><em>Colouring an alignment by conservation</em><br>
46 Conservation scores can be used to colour an alignment. This is
47 explained further in the help page for <a
48 href="../colourSchemes/conservation.html">conservation colouring</a>.