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23 <title>Alignment RNA Structure Consensus Annotation</title>
27 <strong>Alignment RNA Structure Consensus Annotation</strong>
30 <p>The RNA structure consensus displayed below the alignment gives the
31 percentage of valid base pairs per column for the first secondary
32 structure annotation shown on the annotation panel. These values are
33 shown as a histogram labeled "StrucConsensus", where a
34 symbol below each bar indicates whether the majority of base pairs
36 <li>'(' - Watson-Crick (C:G, A:U/T)</li>
37 <li>'[' - Non-canonical (a.ka. wobble) (G:U/T)</li>
38 <li>'{' - Invalid (a.k.a. tertiary) (the rest)</li>
40 <p>Mousing over the column gives the fraction of pairs classified
41 as Watson-Crick, Canonical or Invalid.</p>
44 this calculation includes gaps in columns. You can choose to ignore
45 gaps in the calculation by right clicking on the label
46 "StrucConsensus" to the left of the structure consensus bar
50 <strong>RNA Structure logo</strong><br /> Right-clicking on the
51 label allows you to enable the structure logo. It is very similar to
52 a sequence logo but instead shows the distribution of base pairs.
53 There are two residues per column, the actual column and the
54 interacting base. The opening bracket is always the one on the left
55 side. <br> Like <a href="consensus.html#logo">sequence
56 logos</a>, the relative amount of a specific base pair can be
57 estimated by its size in the logo, and this can be made more obvious
58 by <em>normalising</em> the logo (enabled via the popup menu). When
59 the logo is displayed, the tool tip for a column gives the exact
60 percentages for all base pairs at that position.