<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
--->
-<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>
+ * 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><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>
+ 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.
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff