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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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-<head><title>Alignment RNA Structure Consensus Annotation</title></head>
-<body><p><strong>Alignment RNA Structure Consensus Annotation</strong></p>
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Alignment RNA Structure Consensus Annotation</title>
+</head>
+<body>
+ <p>
+ <strong>Alignment RNA Structure Consensus Annotation</strong>
+ </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>
+ <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><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 it's size in the logo. The tool tip of a column gives the
-exact numbers for all occurring valid base pairs.
-</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
+ "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>
</body>
</html>
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