X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=c194a53b2dbedede99657dbf12cb94be42b53f79;hb=35738b40f315d0f619116f4e0b23e9a8ebf141d2;hp=7325439bc6d1bb20aec9c6473445c3391becb69a;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index 7325439..c194a53 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.
+ +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.
+
- 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. -