\vspace{0.5in}
{\huge
-A Manual with Introductory Tutorial }
+Manual and Introductory Tutorial }
\vspace{2.4in}
\vspace{2in}
-Manual Version 1.5
+Manual Version 1.5.0
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-4th December 2014
+12th December 2014
\end{center}
\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
FASTA, Clustal, MSF(GCG) and PIR.
-There are two types of Jalview program. The {\bf Jalview Desktop} is a stand
-alone application that provides powerful editing, visualization, annotation and
+There are two types of Jalview program. The {\bf Jalview Desktop} is a standalone
+application that provides powerful editing, visualization, annotation and
analysis capabilities. The {\bf JalviewLite} applet has the same core
visualization, editing and analysis capabilities as the desktop, without the
desktop's webservice and figure generation capabilities. It is designed to be
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/}}
The Jalview Desktop can be run in two ways; as an application launched from the
web {\sl via} Java webstart, or as an application loaded onto your hard drive.
The webstart version is launched from the pink `Launch Jalview Desktop
-button' at the top right handside of pages of the website
+button' at the top right hand side of pages of the website
\href{http://www.jalview.org}{(www.jalview.org)}.
To download the locally installable version, follow the links on the download
page
(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
\subsubsection{Jalview News RSS Feed}
Announcements are made available to users of the
-Jalview Desktop {\sl via} the Jalview News reader. This window will open
+Jalview Desktop {\sl via} the Jalview Newsreader. This window will open
automatically when new news is available, and can also be accessed {\sl via} the
Desktop's {\sl Tools $\Rightarrow$ Show Jalview News} menu entry.
\begin{figure}[htbp]
\begin{center}
\includegraphics[height=3in]{images/jvrssnews.pdf}
-\caption{{\bf The Jalview News Reader.} The news reader opens automatically
+\caption{{\bf The Jalview News Reader.} The newsreader opens automatically
when new articles are available from the Jalview Desktop's news channel.}
\label{jalviewrssnews}
\end{center}
site \href{http://www.jalview.org}{(www.jalview.org)}
in your web browser. Launch Jalview by clicking on the
pink `Launch Jalview' Desktop button in the top right hand corner. This
-will download and open a jalview.jnlp webstart file.} \exstep {Dialogue boxes
-will open and ask if you want to open the the jalview.jnlp file as the file is an application downloaded from the
+will download and open a jalview.jnlp webstart file.}
+\exstep {Dialogue boxes
+will open and ask if you want to open the jalview.jnlp file as the file is an application downloaded from the
Internet, click Open. (Note you maybe asked to update Java, if you agree then it
will automatically update the Java software). As Jalview opens, four demo
-Jalview windows automatically load.} \exstep {If
+Jalview windows automatically load.}
+\exstep {If
you are having trouble, it may help changing the browser you are using, as the browsers and
-it's version may effect this process.}
+it's version may affect this process.}
\exstep{To deactivate the opening of the 4 demo sequences during the launch, go
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. A `Preference'
\exstep{To reload the original demo file select the
{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
the URL history button on the right hand side of the dialog box to view the
-files, selected exampleFile-2-7.jar, then click OK.}
+files, select exampleFile\_2\_7.jar, then click OK.}
{\bf Note:} Should you want to reload the example alignment or load your own
sequence during the launch process, then go
to the {\sl Tools $\Rightarrow$
may want to move this from the downloads folder to another folder.
Opening from this file will allow Jalview to be launched offline.
-{\bf Help launching Jalview is avaliable in a video on
+{\bf Help launching Jalview is available in a video on
\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
the website.}}
editing and navigation is performed using the mouse, and {\bf cursor mode}
where editing and navigation are performed using the keyboard. The {\bf F2 key}
is used to switch between these two modes. With a Mac as the F2 is
- often assigned to screen brightness, one maay often need to type {\bf function
+ often assigned to screen brightness, one may often need to type {\bf function
[Fn] key with F2}.
\begin{figure}[htb]
\begin{center}
\includegraphics[width=6.5in]{images/jalview_anatomy.pdf}
-\caption{{\bf The anatomy of Jalview.} The major features of the Jalview Desktop Application are labelled.}
+\caption{{\bf The anatomy of Jalview.} The major features of the Jalview Desktop Application are labeled.}
% TODO: modify text labels to be clearer - black on grey and black border for clarity
\label{anatomy}
\end{center}
\end{figure}
-\subsection{Navigation in Normal mode}
+\subsection{Navigation in Normal Mode}
Jalview always starts up in Normal mode, where the mouse is used to interact
with the displayed alignment view. You can move about the alignment by clicking
$\Rightarrow$ Close All} option from the Jalview desktop.
{\bf \em{Warning: make sure you have saved your work because this cannot be
-undone !}} }
+undone!}} }
\parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
}}
-\subsection{Navigation in Cursor mode}
+\subsection{Navigation in Cursor Mode}
\label{cursormode}
\parbox[c]{5in}{Cursor mode navigation enables the user to quickly
and precisely navigate, select and edit parts of an alignment. On pressing F2 to
window. Select topic from the navigation panel on the left hand side or use the
Search tab to select specific key words
-{\bf Help navigating Jalview is avaliable in a video on
+{\bf Help navigating Jalview is available in a video on
\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
the website.}}
registry. Jalview's sequence fetching capabilities allow you to avoid having to
manually locate and save sequences from a web page before loading them into
Jalview. It also allows Jalview to gather additional metadata provided by the
-source, such as annotation and database cross references.
+source, such as annotation and database cross-references.
Select {\sl File $\Rightarrow$ Fetch Sequence(s) \ldots} from the main menu and
a window will appear (Figure \ref{loadseq}). Pressing the database selection
button in the dialog box opens a new window showing all the database sources
number {\bf PF03460} and click OK. An alignment of about 107 sequences should load.
Several database IDs
-or accession numbers can be loaded by using semicolons to separated them.}}
+or accession numbers can be loaded by using semicolons to separate them.}}
\subsection{Memory Limits}
\label{memorylimits}
PF03460 (see Exercise \ref{load}). } \exstep{
Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a
-location into which to save the alignment and select your prefered format. All
+location into which to save the alignment and select your preferred format. All
formats except {\sl Jalview } jvp can be viewed in a normal text editor (e.g.
Notepad) or in a web browser.
Enter a file name and click {\sl Save}.
Press {\bf Q} to mark this position.
Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
to complete the selection. Note to clear the selection press the {\bf[ESC]}
-key.} \exstep{To create a {\bf group} from the selected the region, click the
-right mouse button when mouse is on the selection, this opens the selection
-popup menu in the alignment window.
+key.}
+\exstep{To create a {\bf group} from the selected the region, click the
+right mouse button when mouse is on the selection, this opens a
+pop-up menu in the alignment window.
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
} menu and select `Percentage Identity'.
to include newly selected sequences, and the `Percentage Identity' colouring changes. } \exstep{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
\exstep{The current selection can be {\bf exported} and saved by right clicking
-on the text area to open the selection popup-menu. Follow the menus and pick an
+on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an
output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
\ldots} submenu.
}
\exercise{Hiding and revealing regions}{
\exstep{Close all windows, open the PFAM accession PF03460. Select a
contiguous set of sequences by clicking and dragging on the sequence ID panel.
-Right click on the selected sequence IDs to bring up the selection pop-up menu, select {\sl Hide Sequences}.
+Right click on the selected sequence IDs to bring up the sequence ID pop-up
+menu, select {\sl Hide Sequences}.
}
\exstep{
Right click on the blue triangle indicating hidden sequences and select {\sl
Repeat the process but use a non-contiguous set of sequences. Note that when
multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
}
-\exstep{Repeat the above using columns to hide and reveale columns
+\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.
}
\exstep{Select a region of the alignment, then add in some additional columns to
the selection, and experiment with the `Hide all but selected region' function
in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
-\exstep{Select some sequences and pick one to represent the rest by hoovering
+\exstep{Select some sequences and pick one to represent the rest by hovering
the mouse over this sequence. Bring up the Sequence ID pop-up menu by right
-clicking and then seelct {\sl (Sequence ID name) $\Rightarrow$ Represent group
+clicking and then select {\sl (Sequence ID name) $\Rightarrow$ Represent group
with (Sequence ID name )}. To reveal these hidden sequences, right click on the
-Sequence ID and in the the pop-up menu select Reveal All.}}
+Sequence ID and in the pop-up menu select Reveal All.}}
+
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit1.pdf}
+\includegraphics[width=3in]{images/edit2.pdf}
+\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
+selected sequence is dragged to the right while pressing and holding [SHIFT].}
+\label{gapseq}
+\end{center}
+\end{figure}
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit3.pdf}
+\includegraphics[width=3in]{images/edit4.pdf}
+\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
+group is dragged to the right with [CTRL] pressed.}
+\label{gapgroup}
+\end{center}
+\end{figure}
\subsubsection{Locked Editing}
\label{lockededits}
The Jalview alignment editing model is different to that used in other alignment
-editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position, editing has the effect of shifting the rest of the sequence(s) being edited down or up-stream with respect to the rest of alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment, but does not avoid the `knock-on' effect which is sometimes undesirable. However, its effect can be limited by performing the edit within a selected region. In this case, gaps will only be removed or inserted within the selected region. Edits are similarly constrained when they occur adjacent to a hidden column.
+editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position,
+editing has the effect of shifting the rest of the sequence(s) being edited down or up-stream with respect to the rest of
+alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment,
+but does not avoid the `knock-on' effect which is sometimes undesirable.
+However, its effect can be limited by performing the edit within a selected region.
+In this case, gaps will only be removed or inserted within the selected region.
+Edits are similarly constrained when they occur adjacent to a hidden column.
-\subsubsection{Introducing Gaps in a Single equence}
+\subsubsection{Introducing Gaps in a Single Sequence}
To introduce a gap, place the cursor on the residue to the immediate right of
where the gap should appear. Hold down the SHIFT key and the left mouse button,
-then drag the sequence to the right untill the required number of gaps has been inserted.
+then drag the sequence to the right until the required number of gaps has been inserted.
One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long. Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
}
\exstep{ Select the first 7 sequences, and press H to hide them (or right click
-on the sequence IDs to open the sequence ID popup menu, and select {\sl Hide
+on the sequence IDs to open the sequence ID pop-up menu, and select {\sl Hide
Sequences}). }
\exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
}
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit1.pdf}
-\includegraphics[width=3in]{images/edit2.pdf}
-\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
-selected sequence is dragged to the right while pressing and holding [SHIFT].}
-\label{gapseq}
-\end{center}
-\end{figure}
-
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit3.pdf}
-\includegraphics[width=3in]{images/edit4.pdf}
-\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
-group is dragged to the right with [CTRL] pressed.}
-\label{gapgroup}
-\end{center}
-\end{figure}
-
-
\subsubsection{Editing in Cursor mode}
-Gaps can be be easily inserted when in cursor mode (toggled with [F2]) by
+Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
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}
or the alignment view's ``background colourscheme'' when no selection exists.
The second method is to select sequences and right click mouse to open pop-up
-menu and seelct {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group
+menu and select {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group
Colour} from context menu options
(Figure \ref{colgrp}). This only changes the colour of the current selection or group.
}\parbox[c]{3in}{
\centerline{\includegraphics[width=2.8in]{images/col_byannot.pdf}}}
-The {\bf per Sequency 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 futher in
-Section \ref{protdisorderpred}.
+rows, such as protein disorder scores. This functionality is described further
+in Section \ref{protdisorderpred}.
\subsection{Colour Schemes}
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.
\section{Alignment Formatting and Graphics Output}
\label{layoutandoutput}
-Jalview is a WYSIWIG alignment editor. This means that for most kinds of graphics output, the layout that is seen on screen will be the same as what is output in an exported graphics file. It is therefore important to pick the right kind of display layout prior to generating figures.
+Jalview is a WYSIWIG alignment editor. This means that for most kinds of graphics output,
+the layout that is seen on screen will be the same as what is outputted in an
+exported graphics file.
+It is therefore important to pick the right kind of display layout prior to generating figures.
\subsection{Multiple Alignment Views}
\subsection{Alignment Layout}
Jalview provides two screen layout modes, unwrapped (the default) where the alignment is in one long line across the window, and wrapped, where the alignment is on multiple lines, each the width of the window. Most layout options are controlled by the Format menu option in the alignment window, and control the overall look of the alignment in the view (rather than just a selected region).
-\subsubsection{Wrapped alignments}
+\subsubsection{Wrapped Alignments}
Wrapped alignments can be toggled on and off using the {\sl Format $\Rightarrow$ Wrap} menu option (Figure \ref{wrap}). Note that the annotation lines are also wrapped. Wrapped alignments are great for publications and presentations but are of limited use when working with large numbers of sequences.
If annotations are not all visible in wrapped mode, expand the alignment window to view them. Note that alignment annotation (see Section \ref{featannot}) cannot be interactively created or edited in wrapped mode, and selection of large regions is difficult.
\parbox[c]{4in}{The text appearance in a view can be modified {\sl via} the {\sl Format $\Rightarrow$ Font\ldots} alignment window menu. This setting applies for all alignment and annotation text except for that displayed in tool-tips. Additionally, font size and spacing can be adjusted rapidly by clicking the middle mouse button and dragging across the alignment window.}
\parbox[c]{2in}{\centerline{\includegraphics[width=1.75in]{images/font.pdf}}}
-\subsubsection{Numbering and label justification}
+\subsubsection{Numbering and Label Justification}
Options in the {\sl Format} menu are provided to control the alignment view, and provide a range of options to control the display of sequence and alignment numbering, the justification of sequence IDs and annotation row column labels on the annotation rows shown below the alignment.
-\subsubsection{Alignment and Group colouring and appearance}
+\subsubsection{Alignment and Group Colouring and Appearance}
The display of hidden row/column markers and gap characters can be turned off with {\sl Format $\Rightarrow$ Hidden Markers} and {\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area behind each residue that is coloured by the applied coloursheme.
-\subsubsection{Highlighting nonconserved symbols}
+\subsubsection{Highlighting Nonconserved Symbols}
The alignment layout and group sub-menu both contain an option to hide
conserved symbols from the alignment display ({\sl Format $\Rightarrow$ Show
nonconserved } in the alignment window or {\sl Selection $\Rightarrow$ Group
The annotation lines which appear below the sequence alignment are described in
detail in Section \ref{featannot}. They can be hidden by toggling the {\sl View
$\Rightarrow$ Show Annotations} menu option. Additionally, each annotation line
-can be hidden and revealed in the same way as sequences {\sl via} the context menu on
-the annotation name panel (Figure \ref{annot}). Annotations can be reordered by
-dragging the annotation line label on the annotation label panel. Placing the
+can be hidden and revealed in the same way as sequences {\sl via} the
+pop-up context menu on the annotation name panel (Figure \ref{annot}).
+Annotations can be reordered by dragging the annotation line label on the annotation label panel. Placing the
mouse over the top annotation label brings up a resize icon on the left. When this is
displayed, Click-dragging up and down provides more space in the alignment window for viewing the annotations, and less space for the sequence alignment.
\exercise{Alignment Layout}{
\label{exscreen}
-\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jar}. Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu. Experiment with the various options from the {\sl Format} menu. to adjust the ruler placement, sequence ID format and so on. }
+\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jar}.
+Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu.
+Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
+sequence ID format and so on. }
\exstep{Hide all the annotation rows by selecting {\sl View $\Rightarrow$ Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.}
-\exstep{{\bf Deselect} {\sl Format $\Rightarrow$ Wrap}, and right click on the annotation row labels to bring up the context menu. Select {\sl Hide This Row}. Bring up the context menu again and select {\sl Show All Hidden Rows} to reveal them}
+\exstep{Deselect {\sl Format $\Rightarrow$ Wrap}. Right click on the
+annotation row labels to bring up the pop-up context menu, then select {\sl
+Hide This Row}. Bring up the pop-up context menu again and select {\sl
+Show All Hidden Rows} to reveal them.}
\exstep{Annotations can be reordered by clicking and dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot} below.}
-\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label - a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed by Clicking and dragging the mouse up or down.}
+\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label -
+a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed
+by clicking and dragging the mouse up or down.}
}
\subsection{Graphical Output}
}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_png.pdf}} \par \centerline{Zoom Detail of PNG image.}}
\exercise{Graphical Output}{
-\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}. Customise it how you wish but leave it unwrapped. Select {\sl File $\Rightarrow$ Export Image $\Rightarrow$ HTML} from the alignment menu. Save the file and open it in your favourite web browser. }
-\exstep{Now wrap the alignment and export the image to HTML again. Compare the two images. Note that the exported image matches the format displayed in the alignment window but {\bf annotations are not exported}.}
-\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ PNG} menu option. Open the file in an image viewer that allows zooming such as Paint or Photoshop (Windows), or Preview (Mac OS X) and zoom in. Notice that the image is a bitmap and it becomes pixelated very quickly. Note also that the {\bf annotation lines are included} in the image.}
+\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}.
+Customise it how you wish but leave it unwrapped.
+Select {\sl File $\Rightarrow$ Export Image $\Rightarrow$ HTML} from the alignment menu.
+Save the file and open it in your favoured web browser. }
+\exstep{Wrap the alignment and export the image to HTML again. Compare the two
+images. (Note that the exported image matches the format displayed in the
+alignment window but {\bf annotations are not exported}).}
+\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ PNG} menu option.
+Open the file in an image viewer that allows zooming such as Paint or Photoshop (Windows), or Preview (Mac OS X) and zoom in.
+Notice that the image is a bitmap and it becomes pixelated very quickly.
+(Note that the {\bf annotation lines are included} in the image.)}
\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image
$\Rightarrow$ EPS} menu option. Open the file in a suitable program such as
Photoshop, Illustrator, Inkscape, Ghostview, Powerpoint (Windows), or
\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
\exercise{Changing the Layout of the Web Services Menu}{
\label{changewsmenulayoutex}
\exstep{Make sure you have loaded an alignment into Jalview, and examine the
-current layout of the alignment windowÔøΩs {\sl Web Service} menu.}
+current layout of the alignment window's {\sl Web Service} menu.}
\exstep{Open the preferences dialog box and select the web services tab.}
\exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
the {\sl Enable Enfin Services} checkboxes.}
Test results from JABAWS are reported on Jalview's console output (opened from
the Tools menu). Tests are re-run every time Jalview starts, and when the
-[Refresh] button is pressed on the Jalview JABAWS configuration panel.
+[Refresh Services] button is pressed on the Jalview JABAWS configuration panel.
\subsubsection{Resetting the JABA services setting to their defaults}
Once you have configured a JABAWS server and selected the OK button of the
The presets are displayed in the JABA web services submenu, and can also be
accessed from the parameter editing dialog box, which is opened by selecting
-the `{\sl Edit settings and run ...}' option from the web serviceÔøΩs menu. If you have used
+the `{\sl Edit settings and run ...}' option from the web services menu. If you have used
a preset, then it will be mentioned at the beginning of the job status file shown
in the web service job progress window.
{\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 / blobdiff