Alignment Conservation Annotation

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 :

Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)).

Conservation is measured as a numerical index reflecting the conservation of physico-chemical properties in the alignment: Identities score highest, and the next most conserved group contain substitutions to amino acids lying in the same physico-chemical class.

Colouring an alignment by conservation
Conservation scores can be used to colour an alignment. This is explained further in the help page for conservation colouring.