Colouring by Conservation
-This is an approach to alignment colouring 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.
-For an already coloured alignment, the conservation index at each - alignment position is used to modify the shading intensity of the - colour at that position. This means that the most conserved columns - in each group have the most intense colours, and the least conserved - are the palest. The slider controls the contrast between these - extremes.
-Conservation can be calculated over the whole alignment, or just - within specific groups of sequences (such as those defined by - phylogenetic tree partitioning). - The option 'apply to all groups' controls whether the contrast - slider value will be applied to the indices for the currently - selected group, or all groups defined over the alignment.
- - + + + ++ Colouring by Conservation +
++ This is an approach to alignment colouring which highlights regions + of an alignment where physicochemical properties are conserved. It + 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)). See the conservation + calculation help page for a more thorough explanation of the + calculation. +
+For an already coloured alignment, the conservation index at + each alignment position is used to modify the shading intensity of + the colour at that position. This means that the most conserved + columns in each group have the most intense colours, and the least + conserved are the palest. The slider controls the contrast between + these extremes.
++ Conservation can be calculated over all sequences in an alignment, + or just within specific groups (such as those defined by phylogenetic tree + partitioning). The option 'apply to all groups' controls whether + the contrast slider value will be applied to the indices for the + currently selected group, or all groups defined over the alignment. +
+ +