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)).

View an HTML version of the paper

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.

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).

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 ! implies that the lack of a particular physicochemical property is conserved (e.g. !proline).

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.

Group conservation
If sequence groups have been defined, then selecting option 'Group Conservation' in the Annotations menu will result in Conservation being calculated for each group, as well as the alignment as a whole.