2 <head><title>Alignment Conservation Annotation</title></head>
3 <body><p><strong>Alignment Conservation Annotation</strong></p>
4 <p>This is an automatically calculated quantitative alignment
5 annotation which measures the number of conserved physico-chemical
6 properties conserved for each column of the alignment. Its calculation
7 is based on the one used in
8 the AMAS method of multiple sequence alignment analysis :<br>
10 C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
11 for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>
15 <p>Conservation is measured as a numerical index reflecting the
16 conservation of physico-chemical properties in the alignment:
17 Identities score highest, and the next most conserved group contain
18 substitutions to amino acids lying in the same physico-chemical
21 <p><em>Colouring an alignment by conservation</em><br>
22 Conservation scores can be used to colour an alignment. This is
23 explained further in the help page for <a
24 href="../colourSchemes/conservation.html">conservation colouring</a>.