X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=c996dc73761eec8c827567ab35aee7d01aec33f2;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=d825463e9c3245be885a6523eb4ee313e018b579;hpb=a90e2fe3cc3b779521a81cf8de410936f3a777c1;p=jalview.git diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index d825463..c996dc7 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -27,28 +27,37 @@ Alignment RNA Structure Consensus Annotation
+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. These + values are shown as a histogram labeled "StrucConsensus", + where a symbol below each bar indicates whether the majority of base + pairs are: +
Mousing over the column gives the fraction of pairs classified + as Watson-Crick, Canonical or Invalid.
+
- 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.
+ By default this calculation includes gaps in columns. You can choose
+ to ignore gaps in the calculation by right clicking on the label
+ "StrucConsensus" 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. -