Conservation Calculation
-This option is based on 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)).
-
- Hierarchical analysis is based on each residue having certain physico-chemical
- properties.
The alignment can first be divided into groups. This is best done by first - creating an average distance tree (Calculate->Average distance tree). Selecting - a position on the tree will cluster the sequences into groups depending on the - position selected. Each group is coloured a different colour which is used for - both the ids in the tree and alignment windows and the sequences themselves. - If a PCA window is visible a visual comparison can be made between the clustering - based on the tree and the PCA.
-The grouping by tree may not be satisfactory and the user may want to edit - the groups to put any outliers together.
-The existing colour scheme is modified so that the most conserved columns in - each group have the most intense colours and the least conserved are the palest
-The conservation analysis is done on each sequence group. This highlights differences - and similarities in conserved residue properties between groups.
- - - + + + ++ 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 :
+
+ 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.
+