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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<strong>Alignment RNA Structure Consensus Annotation</strong>
</p>
+ <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. 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 (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>
- 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.<br>
- The amount of valid base pairs is indicated by the profile in the
- Alignment Annotation row.<br> 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>
+ 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>Structure logo</strong>
- </p>
- 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.
- <br> 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.
+ <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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git://source.jalview.org / jalview.git / blobdiff