X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=9641a8e443f6ccdc57e3fbeb93c22d37edde43a2;hb=45f546c71f94606ab43389d596139606bd001656;hp=421e40f22bf6ed31638c28149b8f6f1d5dd5b1b1;hpb=1693646e78fb0dddebcd94f8bef7e2acd3bdaae0;p=jalview.git diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 421e40f..9641a8e 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,25 +1,54 @@ - -
-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).
+ +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.
+