X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=756e6e961f374626917ae50b9141bcc6d2bb1663;hb=df5ad5c09e166650d21510105f9efc3d25055b08;hp=7325439bc6d1bb20aec9c6473445c3391becb69a;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index 7325439..756e6e9 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -27,28 +27,35 @@ 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.
+
The RNA structure consensus displayed below the alignment gives + the percentage of valid base pairs per column for the first + secondary structure annotation shown on the annotation panel. The + symbol below each histogram indicates whether the majority of base + pairs are: +
Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.
+ +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. -