- 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>
- <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.