X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=756e6e961f374626917ae50b9141bcc6d2bb1663;hb=df5ad5c09e166650d21510105f9efc3d25055b08;hp=4093777306554951c364058ffd1d69438f7fda14;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index 4093777..756e6e9 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -1,45 +1,61 @@ -Alignment RNA Structure Consensus Annotation -

Alignment RNA Structure Consensus Annotation

+ --> + +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 tool tip of a column gives the -exact numbers for all occurring valid base pairs. -

+

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 +

+ Right-clicking on the label allows you to enable the structure logo. + It is very similar to a sequence logo but instead shows the + distribution 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 its size in the logo. When the logo is displayed, + the tool tip of a column gives the exact numbers for all occurring + valid base pairs. +