From df5ad5c09e166650d21510105f9efc3d25055b08 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 21 Sep 2016 16:49:43 +0100 Subject: [PATCH] JAL-1841 JAL-2214 updated RNA Structure Consensus documentation --- help/html/calculations/structureconsensus.html | 45 ++++++++++++++---------- 1 file changed, 26 insertions(+), 19 deletions(-) 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. -
Like sequence logos the relative amount of a specific base - pair can be estimated by its size in the logo. The tool tip of a - column gives the exact numbers for all occurring valid base pairs. + 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.

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