<p>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
+ 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:
<ul>
- <li>'(' - Watson-Crick (A:C, G:T)</li>
- <li>'[' - Canonical Pairs (A:C, G:U, A:U)</li>
- <li>'{' - Invalid Pairs (the rest)</li>
+ <li>'(' - Watson-Crick (C:G, A:U/T)</li>
+ <li>'[' - Non-canonical (a.ka. wobble) (G:U/T)</li>
+ <li>'{' - Invalid (a.k.a. tertiary) (the rest)</li>
</ul>
- <p>Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.</p>
-
-<p>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.<br>
+ <p>Mousing over the column gives the fraction of pairs classified
+ as Watson-Crick, Canonical or Invalid.</p>
+
<p>
- <strong>Structure logo</strong>
- </p>
- 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.
- <br> 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.
+ 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.<br>
+ <p>
+ <strong>RNA Structure logo</strong><br /> 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. <br> Like <a href="consensus.html#logo">sequence
+ logos</a>, 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 <em>normalising</em> 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.
</p>
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