The VARNA RNA Viewer

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fvarna.html;h=029edceab182c6d33074aa7a34c881af05175637;hb=2c2992b8822b686f7f12022a66aa41f6969d06d0;hp=f044a4413a354a9224754fdf21b740e3096ee0e9;hpb=dc507a79f5eb7837ec52343686e84f9d4b56f0fc;p=jalview.git diff --git a/help/html/features/varna.html b/help/html/features/varna.html index f044a44..029edce 100644 --- a/help/html/features/varna.html +++ b/help/html/features/varna.html @@ -1,74 +1,93 @@ - - - -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. - -

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
- Trimed 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 Jmol

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 it's own. Only the -essentials have been described here - the interested reader is -referred to VARNA's own -comprehensive online documentation.

The VARNA RNA Viewer

+ 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

+ 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. +