Alignment RNA Structure Consensus Annotation

From dc507a79f5eb7837ec52343686e84f9d4b56f0fc Mon Sep 17 00:00:00 2001 From: janengelhardt Date: Mon, 22 Aug 2011 01:25:34 +0200 Subject: [PATCH] JAL-913; Extending documentation; VARNA help; Change-Id: If1deae2cf040ac9a28ab770019a0e3040f74daeb --- help/help.jhm | 2 + help/helpTOC.html | 3 +- help/helpTOC.xml | 11 ++- help/html/calculations/consensus.html | 6 ++ help/html/calculations/structureconsensus.html | 44 ++++++++++++ help/html/calculations/structureconservation.html | 28 -------- help/html/features/jmol.html | 2 +- help/html/features/varna.html | 74 +++++++++++++++++++++ 8 files changed, 137 insertions(+), 33 deletions(-) create mode 100755 help/html/calculations/structureconsensus.html delete mode 100755 help/html/calculations/structureconservation.html create mode 100644 help/html/features/varna.html diff --git a/help/help.jhm b/help/help.jhm index 0fd8d65..3c560ab 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -30,6 +30,7 @@ + @@ -75,6 +76,7 @@ + diff --git a/help/helpTOC.html b/help/helpTOC.html index a1d890f..f9945d7 100644 --- a/help/helpTOC.html +++ b/help/helpTOC.html @@ -64,13 +64,14 @@
      Remove Redundancy
   Alignment Annotations
      Conservation -
      RNA Structure Conservation
      Quality
      Consensus +
      RNA Structure Consensus
      Annotations File Format
   Viewing PDB Files
      Jmol Viewer
      Simple PDB Viewer +
   Viewing RNA structures
   VAMSAS Data Exchange
   Window Menus
      Desktop Window diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 2f8a2fd..5371ad4 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -35,7 +35,11 @@ - + + + + + @@ -89,16 +93,17 @@ - - + + + diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index 6a22aef..74bf247 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -30,6 +30,12 @@

Select the "Copy Consensus Sequence" entry from the consensus annotation label to copy the alignment's consensus sequence to the clipboard. + +

Sequence logo

+By clicking on the label you can also activate the sequence logo. It +indicates the relative amount of residues per column which can be +estimated by it's size in the logo. The tooltip of a column gives the +exact numbers for all occuring residues.

diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html new file mode 100755 index 0000000..5f989a5 --- /dev/null +++ b/help/html/calculations/structureconsensus.html @@ -0,0 +1,44 @@ + + +Alignment RNA Structure Consensus Annotation +

Alignment RNA Structure Consensus Annotation

+ +

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.
+The amount of valid base pairs is indicated by the profile in the +Alignment Annotation row.
+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.
+ +

Structure logo

+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.
+Like sequence logos the relative amount of a specific base pair can be +estimated by it's size in the logo. The tooltip of a column gives the +exact numbers for all occuring valid base pairs. +

+ + diff --git a/help/html/calculations/structureconservation.html b/help/html/calculations/structureconservation.html deleted file mode 100755 index c632db5..0000000 --- a/help/html/calculations/structureconservation.html +++ /dev/null @@ -1,28 +0,0 @@ - - -Alignment RNA Structure Conservation Annotation -

Alignment RNA Structure Conservation Annotation

This is an automatically calculated quantitative alignment -annotation which measures the number of conserved base pairs in -relation to a secondary structure. The canonical Watson-Crick base -pairings (A-T/U, G-C) and the wobble base pair (G-T/U) are regarded as -valid pairings.
-The amount of valid base pairs is indicated by the profile in the Alignment Annotation row. - - diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index d23e1d6..0fc9b1c 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -23,7 +23,7 @@

The Jmol PDB Viewer

Since Jalview 2.3, Jmol has been integrated into Jalview for interactively viewing structures -opened by selecting the "Sequence→View PDB +opened by selecting the "Structure→View PDB entry:" option in the sequence id pop-up menu (if you can't see this, then you need to associate a PDB structure with the diff --git a/help/html/features/varna.html b/help/html/features/varna.html new file mode 100644 index 0000000..f044a44 --- /dev/null +++ b/help/html/features/varna.html @@ -0,0 +1,74 @@ + + + +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.
+ + -- 1.7.10.2