X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;fp=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=5f989a5cf3b5273ff68cb4fde9458bfc02449a1e;hb=dc507a79f5eb7837ec52343686e84f9d4b56f0fc;hp=0000000000000000000000000000000000000000;hpb=04d2166bf6e1ae6df7fb0e346d228b69a8e8a089;p=jalview.git diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html new file mode 100755 index 0000000..5f989a5 --- /dev/null +++ b/help/html/calculations/structureconsensus.html @@ -0,0 +1,44 @@ + + +Alignment RNA Structure Consensus Annotation +

Alignment RNA Structure Consensus Annotation

+ +

The RNA structure consensus displayed below the alignment is the +percentage of valid base pairs per column. It is calculated in +relation to a secondary structure and just paired columns are +calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) and +the wobble base pair (G-T/U) are regarded as valid pairings.
+The amount of valid base pairs is indicated by the profile in the +Alignment Annotation row.
+By default this calculation includes gaps in columns. You can choose +to ignore gaps in the calculation by right clicking on the label +"StrConsensus" to the left of the structure consensus bar +chart.
+ +

Structure logo

+By clicking on the label you can also activate the structure logo. It is very +similar to a sequence logo but counts the numbers of base pairs. There +are two residues per column, the actual column and the interacting +base. The opening bracket is always the one on the left side.
+Like sequence logos the relative amount of a specific base pair can be +estimated by it's size in the logo. The tooltip of a column gives the +exact numbers for all occuring valid base pairs. +

+ +