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-<head>
-<title>Alignment Conservation Annotation</title>
-</head>
-<body>
- <p>
- <strong>Alignment Conservation Annotation</strong>
- </p>
- <p>
- This is an automatically calculated quantitative alignment
- annotation which measures the number of conserved physico-chemical
- properties conserved for each column of the alignment. Its
- calculation is based on the one used in the AMAS method of multiple
- sequence alignment analysis :<br>
- <ul>
- Livingstone C.D. and Barton G.J. (1993), Protein Sequence
- Alignments: A Strategy for the Hierarchical Analysis of Residue
- Conservation.
- <em>CABIOS</em> Vol.
- <b>9</b> No. 6 (745-756)).
- </ul>
- <em><a
- href="http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html">View
- an HTML version of the paper</a></em>
- </p>
- <p>
- Conservation is measured as a numerical index reflecting the
- conservation of <a href="../misc/aaproperties.html">physico-chemical
- properties</a> in the alignment: Identities score highest, and the
- next most conserved group contain substitutions to amino acids lying
- in the same physico-chemical class.
- </p>
- <p>Conservation is visualised on the alignment or a sequence group
- as a histogram giving the score for each column. Conserved columns
- are indicated by '*' (score of 11 with default amino acid property
- grouping), and columns with mutations where all properties are
- conserved are marked with a '+' (score of 10, indicating all
- properties are conserved).</p>
- <p>
- Mousing over a conservation histogram reveals a tooltip which
- contains a series of symbols corresponding to the physicochemical
- properties that are conserved amongst the amino acids observed at
- each position. In these tooltips, the presence of <em>!</em> implies
- that the lack of a particular physicochemical property is conserved
- (e.g. !proline).
- </p>
- <p>
- <strong>Colouring an alignment by conservation</strong><br>
- Conservation scores can be used to colour an alignment. This is
- explained further in the help page for <a
- href="../colourSchemes/conservation.html">conservation
- colouring</a>.
- </p>
- <p>
- <strong>Group conservation</strong><br> If sequence groups have
- been defined, then selecting option 'Group Conservation' in the <a
- href="../menus/alwannotation.html">Annotations menu</a> will
- result in Conservation being calculated for each group, as well as
- the alignment as a whole.
- </p>
-</body>
-</html>
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