X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fvarna.html;h=0ce31398c7a715af9108d5e11244c9d9ae028512;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9cf574a6b6d234404df9ff7265237dbbb5e27a60;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
The VARNA RNA Viewer
-The VARNA RNA Viewer
-Since Jalview
-2.7.1, VARNA has been
-integrated into Jalview for interactively viewing structures opened by
-selecting the "Structure→View
-Structure:" option in
-the sequence id pop-up menu (if
-you can't see this, then no RNA structure is associated with your
-sequence or alignment. In the pop-up menu all structures that
-are associated with this sequence and all sequences that are
-associated with the alignment are available.
+
+ The VARNA RNA Viewer
+
+
+ VARNA was integrated
+ into Jalview 2.8 to allow interactive viewing of RNA secondary
+ structure annotation. It is opened by selecting the "Structure→View
+ Structure:" option in the sequence
+ id pop-up menu (if you can't see this, then no RNA structure is
+ associated with your sequence or alignment). In the pop-up menu all
+ structures that are associated with this sequence and all sequences
+ that are associated with the alignment are available.
+
+ Saving a Jalview session as a project file includes the state of any
+ Varna viewers, which are reopened when the project is reloaded (since
+ Jalview 2.9).
+
+ Different structures
+
+
+ - Alignment structures: Structures associated with the
+ alignment are marked by having "consensus" attached to
+ their name. VARNA contains two different entries for consensus
+ structures.
+
+ - Consensus structure: the individual sequence folded
+ into the consensus structure
+ - Trimmed consensus structure: the individual sequence
+ folded into the the gap-free consensus structure. That means
+ all columns that contained gaps in the individual sequence
+ were removed. If this breaks a base-pair the pairing is
+ removed also. This can be considered as an approximation for
+ the individual structure.
+
+ - Individual structures: this is a structure
+ associated with the individual sequence and therefore not related
+ to the alignment
+
+
+ Controls
+
+ - Rotate view - Left Click and drag
+ - Zoom in - Press '+'
+ - Zoom out - Press '-'
+ - Choose a different structure - Left click on structure in
+ the left hand panel
+ - Highlighting bases - Move mouse over columns in the Jalview
+ alignment panel
+
-Different structures
-
- -
- Alignment structures:
- Structures associated with the alignment are marked by having "consensus" attached to their name. VARNA contains two different entries for consensus structures.
-
- - Consensus structure: the individual sequence folded into the consensus structure
- - Trimmed consensus structure: the individual sequence
- folded into the the gap-free consensus structure. That means all
- columns that contained gaps in the individual sequence were
- removed. If this breaks a base-pair the pairing is removed also.
- This can be considered as an approximation for the individual structure.
-
-
- -
- Individual structures:
- this is a structure associated with the individual sequence and therefore not related to the alignment
-
-
-Controls
-
-- Rotate view - Left Click and drag
-- Zoom in - Press '+'
-- Zoom out - Press '-'
-- Choose a different structure - Left click on structure in the left hand panel
-- Highlighting bases - Move mouse over columns in the Jalview alignment panel
-
-
-Functionality provided by VARNA
-VARNA's own functions are accessed by right-clicking in the
-structure display area. That will open the VARNA pop-up menu,
-which provides access to a number of features like different draw algorithm, color highlighting or annotations.
-
-More Information
-VARNA is a very powerful RNA viewer on its own. Only the
-essentials have been described here - the interested reader is
-referred to VARNA's own
-comprehensive online documentation.
+
+ Functionality provided by VARNA
+
+ VARNA's own functions are accessed by right-clicking in the
+ structure display area. That will open the VARNA pop-up menu, which
+ provides access to a number of features like different draw
+ algorithm, color highlighting or annotations.
+
+ More Information
+
+
+ VARNA is a very powerful RNA viewer on its own. Only the essentials
+ have been described here - the interested reader is referred to VARNA's own comprehensive online documentation.
+