\vspace{0.5in}
{\huge
-Manual with Introductory Tutorial }
+Manual and Introductory Tutorial }
\vspace{2.4in}
\subsection{Jalview}
Jalview is a multiple sequence alignment viewer, editor and analysis tool.
Jalview is designed to be platform independent (running on Mac, MS Windows, Linux
-and any other platforms that supports Java). Jalview is capable of editing and
+and any other platforms that support Java). Jalview is capable of editing and
analysing large alignments (thousands of sequences) with minimal degradation in
performance, and able to show multiple integrated views of the alignment and
other data. Jalview can read and write many common sequence formats including
embedded in a web page,\footnote{A demonstration version of Jalview (Jalview Micro
Edition) also runs on a mobile phone but the functionality is limited to sequence
colouring.} and includes a javascript API to allow customisable display of alignments for web sites such as
-{\bf Pfam}.\footnote{\url{http://pfam.sanger.ac.uk}}
+{\bf Pfam}.\footnote{\url{http://pfam.xfam.org}}
Jalview 2.8.2 was released in December 2014. The Jalview Desktop in this version
visualization of sequence alignments, and their interactive analysis. Tree
building, principal components analysis, physico-chemical property conservation
and sequence consensus analyses are built into the program. Web services enable
-Jalview to access on line alignment and secondary structure prediction programs,
+Jalview to access online alignment and secondary structure prediction programs,
as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
\begin{figure}[htbp]
\begin{center}
between Jalview, TOPALi and AstexViewer.} in 2004, enabling Andrew Waterhouse and
Jim Procter to re-engineer the original program to introduce contemporary developments
in bioinformatics and take advantage of the latest web and Java technology.
-Jalview's development was supported from 2009
-by an award from the BBSRC's Tools and Resources fund. Jalview's development is
-currently being funded by a BBSRC `Extending The Jalview Resource for
-Biological Sequence Alignment and Analysis' grant and a Wellcome Trust
-`Extending The Jalview Resource for Biological Sequence Alignment and Analysis'
-grant. In 2010, 2011, and 2012, Jalview benefitted from the
+Jalview's development has been supported from 2009
+by awards from the BBSRC's Tools and Resources fund, and, since 2014, a Wellcome Trust Biomedical Resource grant\footnote{Wellcome grant number 101651/Z/13/Z}. In 2010, 2011, and 2012, Jalview benefitted from the
\href{http://code.google.com/soc/}{Google Summer of Code}, when Lauren Lui and Jan Engelhardt introduced new features for handling RNA alignments and secondary structure annotation, in collaboration with Yann Ponty.\footnote{\url{http://www.lix.polytechnique.fr/~ponty/}}
(Figure \ref{download}).
These links will launch the latest stable release of Jalview.\par
+%% this paragraph needs to be rewritten for the new signed certificate from Certum.
+
When the application is launched with webstart, two dialogs may appear before
the application starts. If your browser is not set up to handle webstart, then
clicking the launch link may download a file that needs to be opened
displayed, and you may have to disable it using the {\sl View $\Rightarrow$
Show Features} option before you can see your colourscheme.
-There are two main types of colouring styles: {\bfsimple static residue}
-colourschemes and {\bfdynamic schemes} which use conservation and consensus
-analysis to control colouring. A {\bfhybrid colouring} is also possible, where
+There are two main types of colouring styles: {\bf simple static residue}
+colourschemes and {\bf dynamic schemes} which use conservation and consensus
+analysis to control colouring. {\bf Hybrid colouring} is also possible, where
static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below.
\subsection{Colouring the Whole Alignment}
}\parbox[c]{3in}{
\centerline{\includegraphics[width=2.8in]{images/col_byannot.pdf}}}
-The {\bf per Sequenc only} option in the {\bf Colour By Annotation} dialog
+The {\bf per Sequence} option in the {\bf Colour By Annotation} dialog
allows each sequence to be shaded according to sequence associated annotation
rows, such as protein disorder scores. This functionality is described further
in Section \ref{protdisorderpred}.
Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. Note the colour change. Now try all the other colour schemes in the {\sl Colour} menu. Note that some colour schemes do not colour all residues.
}
\exstep{
-Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group of around 4 similar sequences. Use the context menu (right click on the group) option {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour $\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which were not coloured are now coloured. The calculations performed for dynamic colouring schemes like Blosum62 are based on the group being coloured, not the whole alignment (this also explains the colouring changes observed in exercise \ref{exselectgrpcolour} during the group selection step).
+Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group
+of around 4 similar sequences. Use the context menu (right click on the group)
+option {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour
+$\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which
+were not coloured are now coloured. The calculations performed for dynamic
+colouring schemes like Blosum62 are based on the group being coloured, not the
+whole alignment (this also explains the colouring changes observed in exercise
+\ref{exselect} during the group selection step).
}
\exstep{
Keeping the same selection as before, colour the complete alignment using {\sl Colour $\Rightarrow$ Taylor}. Select the menu option {\sl Colour $\Rightarrow$ By Conservation}. Slide the selector from side to side and observe the changes in the alignment colouring in the selection and in the complete alignment.
\subsection{Viewing Structures}
+\label{viewAllStructures}
The structure viewer can be launched in two ways from the sequence ID context
menu. To view a particular structure associated with a sequence in the
alignment, simply select it from popup menu's associated structures submenu in
\exercise{Colouring a protein complex to explore domain-domain interfaces}{\label{dnmtcomplexex}
\exstep{Download the PDB file at
-\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop. This
-is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA server.}
+\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop.
+
+This is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA
+server.}
\exstep{Launch the Jalview desktop and ensure you have at least 256MB of
free memory available.
{\sl Use the following webstart link:
-\href{http://www.jalview.org/webstart/jalview_1G.jnlp}{http://www.jalview.org/webstart/jalview\_1G.jnlp}}.}
+
+\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}}
\exstep{Retrieve the following
{\bf full} PFAM alignments: PF02008, PF00145, PF01426 (make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.}
\exstep{Drag the structure you downloaded in
in the structure.}}
\exstep{Save your work as a Jalview project and verify that it can be opened again by starting another Jalview Desktop instance, and dragging the saved project into the desktop window.}
-{\sl Note: This exercise relies on new features introduced in Jalview 2.7. If
-you notice any strange behaviour when trying out this exercise, it may be a
-bug (see
-\href{http://issues.jalview.org/browse/JAL-1008}{http://issues.jalview.org/browse/JAL-1008}
-for one relating to highlighting of positions in the alignment window).} }
+% {\sl Note: This exercise relies on new features introduced in Jalview 2.7. If
+% you notice any strange behaviour when trying out this exercise, it may be a
+% bug (see
+% \href{http://issues.jalview.org/browse/JAL-1008}{http://issues.jalview.org/browse/JAL-1008}
+% for one relating to highlighting of positions in the alignment window).}
+}
\section{Analysis of alignments}
\label{alignanalysis}
\exercise{Trees}{
-\exstep{Ensure that you have at least 1G memory available in Jalview (start with this link: \href{http://www.jalview.org/webstart/jalview_1G.jnlp}{http://www.jalview.org/webstart/jalview\_1G.jnlp}).}
+\exstep{Ensure that you have at least 1G memory available in Jalview (start with this link: \href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}).}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour. Place the cursor to give about 4 groups, then select {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are reordered to match the order in the tree and groups are formed implicitly.}
\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring makes it easy to see the diferences between the two trees, calculated using different methods.}
\exercise{Remove redundant sequences}{
-{\sl Note: Jalview 2.8 users - bugs in this version mean that the 'Unlinked leaves' markings will not be shown when sequences are removed during this exercise.}
-
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
\exstep{Open the Remove Redundancy dialog and adjust the threshold to 90\%. Remove the sequences that are more than 90\% similar under this alignment.}
\subsection{One-way web services}
-There are three types of one way service in jalview. Database services,
+There are two types of one way service in jalview. Database services,
which were introduced in in Section \ref{fetchseq}, provide sequence and
alignment data. They can also be used to add sequence IDs to an alignment
imported from a local file, prior to further annotation retrieval, as described
in Section \ref{featuresfromdb}. A second type of one way service is provided
by Jalview's DAS sequence feature retrieval system, which is described
-in Section \ref{dasfretrieval}. The final type of one way service are sequence
-and ID submission services, exemplified by the `Envision2 Services' provided
-by the ENFIN Consortium\footnote{ENFIN is the European Network for Functional
-INtegration. Please see http://www.enfin.org for more information. }.
-
-\subsubsection{One-way submission services}
-Jalview can use the system's web browser to submit sets of sequences and
-sequence IDs to web based applications. Single sequence IDs can be passed to
-a web site using the user definable URL links listed under the {\sl
-Links} submenu of the sequence ID popup menu. These are configured
-in the {\sl Connections} tab of the {\sl Preferences} dialog box.
-
-The Envision 2 services presented in the webservice menu provides are the first
-example of one-way services where multiple sequences or sequence IDs can be
-sent. The {\sl Web service $\Rightarrow$ Envision 2 Services} menu entry
-provides two sub-menus that enable you to submit the sequences or IDs
-associated with the alignment or just the currently selected sequences to one
-of the Envision2 workflows. Selecting any one will open a new browser window on
-the Envision2 web application. The menu entries and their tooltips provide
-details of the Envision2 workflow and the dataset set that will be submitted
-({\sl i.e.} the database reference type, or associated sequence subset). Please
-note, due to technical limitations, Jalview can currently only submit small
-numbers of sequences to the workflows - if no sequence or ID submissions are
-presented in the submenus, then try to select a smaller number of sequences to
-submit.
+in Section \ref{dasfretrieval}.
+% The final type of one way service are sequence
+% and ID submission services.
+% exemplified by the `Envision2 Services' provided
+% by the ENFIN Consortium\footnote{ENFIN is the European Network for Functional
+% INtegration. Please see http://www.enfin.org for more information. }.
+
+% \subsubsection{One-way submission services}
+% Jalview can use the system's web browser to submit sets of sequences and
+% sequence IDs to web based applications. Single sequence IDs can be passed to
+% a web site using the user definable URL links listed under the {\sl
+% Links} submenu of the sequence ID popup menu. These are configured
+% in the {\sl Connections} tab of the {\sl Preferences} dialog box.
+%
+% The Envision 2 services presented in the webservice menu provides are the first
+% example of one-way services where multiple sequences or sequence IDs can be
+% sent. The {\sl Web service $\Rightarrow$ Envision 2 Services} menu entry
+% provides two sub-menus that enable you to submit the sequences or IDs
+% associated with the alignment or just the currently selected sequences to one
+% of the Envision2 workflows. Selecting any one will open a new browser window on
+% the Envision2 web application. The menu entries and their tooltips provide
+% details of the Envision2 workflow and the dataset set that will be submitted
+% ({\sl i.e.} the database reference type, or associated sequence subset). Please
+% note, due to technical limitations, Jalview can currently only submit small
+% numbers of sequences to the workflows - if no sequence or ID submissions are
+% presented in the submenus, then try to select a smaller number of sequences to
+% submit.
\subsection{Remote Analysis Web Services}
Remote analysis services enable Jalview to use external computational
{\sl Note: you may want to keep this data for use in exercise \ref{viewannotfileex}.}
}
-}
+\exstep{
+In the original alignment that you loaded in step 1, {\bf select all} sequences,
+then open the {\bf Sequence ID $\Rightarrow$ Selection } submenu and select the
+{\bf Add Reference Annotation} option.
+
+The JNet predictions for the sequences should now be visible in the original
+alignment.} }
\section{Protein Disorder Prediction}
\label{protdisorderpred}
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5in]{images/disorderpredannot.pdf}
-\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disorderd regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
+\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A
+zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disordered regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
\label{alignmentdisorderannot}
\end{center}
\end{figure}
by default, but can be shown by right-clicking on the alignment
annotation panel and selecting \textbf{Show hidden annotation}.
+\exercise{Protein Disorder Prediction}{
+\label{protdispredex}
+
+\exstep{Open the alignment at
+\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
+
+\exstep{Run the DISEMBL disorder predictor {\slvia} the {\slWeb Services
+$\Rightarrow$ Disorder Prediction } submenu.}
+
+\exstep{Use {\sl Sequence ID $\Rightarrow$ Structure $\Rightarrow$ Discover PDB
+IDs} to retrieve all the PDB structures for the sequences.}
+
+\exstep{Open and align
+the structures for all sequences.
+
+{\sl Hint: see \ref{viewAllStructures} to see how to do this.}}
+
+\exstep{Compare the disorder predictions to the structure data by mapping any
+available temperature factors to the alignment {\sl via} the {\sl Sequence ID
+Popup $\Rightarrow$ Selection $\Rightarrow$ Add reference annotation} option.}
+
+\exstep{Apply the IUPred disorder prediction method}
+\exstep{Use the {\sl Per
+sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog to shade
+the sequences by the long and short disorder predictors.
+Do the two methods agree with the structure ?}}
+
\section{Features and Annotation}
\label{featannot}
Features and annotations are additional information that is overlaid on the sequences and the alignment. Generally speaking, annotations are associated with columns in the alignment. Features are associated with specific residues in the sequence.
\label{featuresfromdb}
Jalview supports feature retrieval from public databases either directly or {\sl
via} the Distributed Annotation System (DAS\footnote{http://www.biodas.org/}).
-It includes built in parsers for Uniprot and EMBL records retrieved from the
-EBI. Sequences retrieved from these sources using the sequence fetcher (see
+It includes built in parsers for Uniprot and ENA (or EMBL) records retrieved
+from the EBI. Sequences retrieved from these sources using the sequence fetcher (see
Section \ref{fetchseq}) will already possess features.
\subsection{Sequence Database Reference Retrieval}
Following DAS feature retrieval, the {\sl Feature Settings} panel takes on a
slightly different appearance (Figure \ref{das} (right)). Each data source is
listed and groups of features from one data source can be selected/deselected
-by checking the labeled box at the top of the panel.
+by checking the labelled box at the top of the panel.
\subsubsection{The Fetch Uniprot IDs dialog box}
then only features found in that region of the alignment will be used to
create the new alignment ordering.
-\exercise{Shading and sorting alignments using sequence features}{
-\label{shadingorderingfeatsex}
-\exstep{Re-load the alignment from \ref{dasfeatretrexcercise}.
-}
-\exstep{Open the
-feature settings panel, and, after first clearing the current
-selection, press the {\em Seq Sort by Density} button a few times.}
-\exstep{Use the DAS fetcher to retrieve the Kyte and Doolittle Hydrophobicity
-scores for the protein sequences in the alignment.
-{\sl Hint: the nickname for the das source is `KD$\_$hydrophobicity'.}}
-\exstep{Change the feature settings so only the hydrophobicity features are
-displayed. Mouse over the annotation and also export and examine the GFF and
-Jalview features file to better understand how the hydrophobicity measurements
-are recorded.}
-\exstep{Apply a {\sl Graduated Colour} to the hydrophobicity annotation to
-reveal the variation in average hydrophobicity across the alignment.}
-\exstep{Select a range of alignment columns, and use one of the sort by feature buttons to order the alignment according to that region's average
-hydrophobicity.}
-\exstep{Save the alignment as a project, for use in exercise
-\ref{threshgradfeaturesex}.} }
-
-\exercise{Shading alignments with combinations of graduated feature
-colourschemes}{
-\label{threshgradfeaturesex}
-\exstep{Reusing the annotated alignment from exercise
-\ref{shadingorderingfeatsex}, experiment with the colourscheme threshold to
-highlight the most, or least hydrophobic regions. Note how the {\sl Colour} icon for the {\sl Feature Type} changes when you change the threshold type and press OK.}
-\exstep{Change the colourscheme so
-that features at the threshold are always coloured grey, and the most
-hydrophobic residues are coloured red, regardless of the threshold value
-({\em hint - there is a switch on the dialog to do this for you}).}
-\exstep{Enable the Uniprot {\em chain} annotation in the feature settings
-display and re-order the features so it is visible under the hydrophobicity
-annotation.}
-\exstep{Apply a {\sl Graduated Colour} to the {\em chain}
-annotation so that it distinguishes the different canonical names associated
-with the mature polypeptide chains.}
-\exstep{Export the alignment's sequence features using the Jalview and GFF file formats, to see how the different types of graduated feature
-colour styles are encoded. }
-}
+% \exercise{Shading and sorting alignments using sequence features}{
+% \label{shadingorderingfeatsex}
+%
+% This exercise is currently not included in the tutorial because no DAS servers
+% currently exist that yield per-residue features for any Uniprot sequence.
+%
+% \exstep{Re-load the alignment from \ref{dasfeatretrexcercise}.
+% }
+% \exstep{Open the
+% feature settings panel, and, after first clearing the current
+% selection, press the {\em Seq Sort by Density} button a few times.}
+% \exstep{Use the DAS fetcher to retrieve the Kyte and Doolittle Hydrophobicity
+% scores for the protein sequences in the alignment.
+% {\sl Hint: the nickname for the das source is `KD$\_$hydrophobicity'.}}
+% \exstep{Change the feature settings so only the hydrophobicity features are
+% displayed. Mouse over the annotation and also export and examine the GFF and
+% Jalview features file to better understand how the hydrophobicity measurements
+% are recorded.}
+% \exstep{Apply a {\sl Graduated Colour} to the hydrophobicity annotation to
+% reveal the variation in average hydrophobicity across the alignment.}
+% \exstep{Select a range of alignment columns, and use one of the sort by feature buttons to order the alignment according to that region's average
+% hydrophobicity.}
+% \exstep{Save the alignment as a project, for use in exercise
+% \ref{threshgradfeaturesex}.} }
+%
+% \exercise{Shading alignments with combinations of graduated feature
+% colourschemes}{
+% \label{threshgradfeaturesex}
+% \exstep{Reusing the annotated alignment from exercise
+% \ref{shadingorderingfeatsex}, experiment with the colourscheme threshold to
+% highlight the most, or least hydrophobic regions. Note how the {\sl Colour} icon for the {\sl Feature Type} changes when you change the threshold type and press OK.}
+% \exstep{Change the colourscheme so
+% that features at the threshold are always coloured grey, and the most
+% hydrophobic residues are coloured red, regardless of the threshold value
+% ({\em hint - there is a switch on the dialog to do this for you}).}
+% \exstep{Enable the Uniprot {\em chain} annotation in the feature settings
+% display and re-order the features so it is visible under the hydrophobicity
+% annotation.}
+% \exstep{Apply a {\sl Graduated Colour} to the {\em chain}
+% annotation so that it distinguishes the different canonical names associated
+% with the mature polypeptide chains.}
+% \exstep{Export the alignment's sequence features using the Jalview and GFF file formats, to see how the different types of graduated feature
+% colour styles are encoded. }
+% }
\section{Working with DNA}
\label{workingwithnuc}
Jalview was originally developed for the analysis of protein sequences, but
sequence fetcher (see Section \ref{fetchseq}) are also parsed in order to
identify codon regions and extract peptide products. Furthermore, Jalview
records mappings between protein sequences that are derived from regions of a
-nucleotide sequence. Mappings are used to to transfer annotation between
+nucleotide sequence. Mappings are used to transfer annotation between
nucleic acid and protein sequences, and to dynamically highlight regions in
one sequence that correspond to the position of the mouse pointer in another.
%TODO Working with Nucleic acid sequences and structures.
for nucleotide alignment. Generally, all will work, but some may be more suited
to your purposes than others. We also note that none of these include
support for taking RNA secondary structure prediction into account when aligning
-sequences. We expect that in the future, Jalview will fully support secondary
-structure aware RNA alignment.
-
+sequences (but will be providing services for this in the future!).
\begin{table}{}
\centering
\begin{tabular}{|l|c|l|}
\exercise{Visualizing protein features on coding regions}
{
-\exstep{Use the sequence fetcher to retrieve EMBL record V00488.}
+\exstep{Use the sequence fetcher to retrieve EMBL record D49489.}
\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the alignment view format to Wrapped mode so the distinct exons can be seen.}
-\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots} window and fetch features for V00488 from the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
+\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots} window and fetch features for D49489 from the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
\exstep{Mouse over the features retrieved, note that they have been mapped onto the coding regions, and in some cases broken into several parts to cover the distinct exons.}
\exstep{Open a new alignment view containing the Uniprot protein product with {\sl Calculate $\Rightarrow$ Get Cross References $\Rightarrow$ Uniprot } and examine the database references and sequence features. Experiment with the interactive highlighting of codon position for each residue.
}
% \subsection{Working with Modeller files}
% \subsection{Using local PDB files}
% \section{Pairwise alignments}
+\subsection{Working with RNA}
+Jalview allows the creation of RNA secondary structure annotation, and includes
+the VARNA secondary structure viewer for the display of RNA base pair diagrams.
+It also allows the extraction of RNA secondary structure from 3D data when
+available.
+
+\subsection{Performing RNA secondary structure predictions}
+Secondary structure consensus calculations can be performed by enabling the
+VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+Structure} menu. These consensus structures are created by analysing the
+covariation patterns in all visible sequences on the alignment. For more
+information see the VIENNA documentation.
+
+\begin{figure}[htbp]
+\begin{center}
+\label{rnaviennaservice}
+\includegraphics[width=5in]{images/rnaViennaServiceWindow.pdf}
+
+\caption{Secondary structure consensus calculations can be performed by enabling the
+VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+Structure} menu.}
+
+\end{center}
+\end{figure}
+
+\begin{figure}[htbp]
+\begin{center}
+\label{rnaviennaaltpairs}
+\includegraphics[width=5in]{images/rnaViennaAlternateProbs.pdf}
+
+\caption{VIENNA can calculate alternate RNA base pairing probabilities. These
+are shown in Jalview as tool-tips on the RNA secondary structure probability
+score.}
+
+\end{center}
+\end{figure}
+
+
+\exercise{Viewing RNA structures}{
+\label{viewingrnaex}
+
+\exstep{Import RF00162 from Rfam (Full).}
+\exstep{Select {\sl Colour by RNA Helices} to shade the alignment by
+the secondary structure annotation provided by Rfam.}
+\exstep{Open VARNA with {\sl Structure $\Rightarrow$ View Structure
+$\Rightarrow$ RNA Secondary Structure}.
+
+ Explore the difference between trimmed and untrimmed views for the
+ structure.
+}
+\exstep{Add and link a Jmol structure view
+for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
+structure along-side the consensus structure for the alignment by adding
+reference annotation from the 3D structure.
+
+{\sl Hint: You need to make sure the RNAview service is enabled in your {\sl
+Structure} preferences to obtain RNA secondary structure annotation from PDB
+files.}}
+
+\exstep{Perform a secondary structure prediction. Enable the VIENNA consensus
+calculation via the {\sl Web Services} menu. Compare this with the annotation
+line provided by Rfam.}
+
+\exstep{Edit the VIENNA calculation settings to show
+Base Pair probabilities.
+
+Explore how editing the alignment affects the consensus
+calculation.} }
+
- \end{document}
+\end{document}
git://source.jalview.org / jalview-manual.git / commitdiff