X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=c194a53b2dbedede99657dbf12cb94be42b53f79;hb=35738b40f315d0f619116f4e0b23e9a8ebf141d2;hp=4093777306554951c364058ffd1d69438f7fda14;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index 4093777..c194a53 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -1,45 +1,63 @@ -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.
+

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.

-

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. -

+

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.
+ +

+ RNA 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, and this can be made more obvious + by normalising the logo (enabled via the popup menu). When + the logo is displayed, the tool tip for a column gives the exact + percentages for all base pairs at that position. +