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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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