% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-3rd February 2017
+15th February 2017
\end{center}
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 and Chimera structure displays,
+Alignment views are dynamically linked with Jmol and UCSF Chimera\footnote{UCSF Chimera needs to be installed separately. It is available free for academic use from \url{https://www.cgl.ucsf.edu/chimera/download.html}.} 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.
\subsection{About this Tutorial }
This tutorial is written in a manual format with short exercises where
-appropriate, typically at the end of each section. This concerns the
+appropriate, typically at the end of each section. The first few sections concerns the
basic operation of Jalview and should be sufficient for those who want to
launch Jalview (Section \ref{startingjv}), open an alignment (Section
\ref{loadingseqs}), perform basic editing (Section
\ref{selectingandediting}), colouring (Section \ref{colours}), and produce
publication and presentation quality graphical output (Section \ref{layoutandoutput}).
-In addition, the manual covers the additional visualization and
-analysis techniques available in Jalview. This includes working
-with the embedded Jmol molecular structure viewer and opening Chimera, building
-and viewing trees and PCA plots, and using trees for sequence conservation analysis. An overview of
+The remaining sections of the manual cover the visualization and
+analysis techniques available in Jalview. These include working
+with the embedded Jmol molecular structure viewer (or UCSF Chimera), building
+and viewing trees and Principal Components Analysis (PCA) plots, and using
+trees for sequence conservation analysis. An overview of
the Jalview Desktop's webservices is given in Section \ref{jvwebservices}, and
the alignment and secondary structure prediction services are described
in detail in Sections \ref{msaservices} and \ref{protsspredservices}
Keystrokes using the special non-symbol keys are represented in the tutorial by
enclosing the pressed keys with square brackets ({\em e.g.} [RETURN] or [CTRL]).
-Keystroke combinations are combined with a `-' symbol ({\em e.g.} [CTRL]-C means
-press [CTRL] and the `C' key) simultaneously.
+Keystroke combinations are denoted with a `-' symbol ({\em
+e.g.} [CTRL]-C means press [CTRL] and the `C' key simultaneously).
Menu options are given as a path from the menu
that contains them - for example {\sl File $\Rightarrow$ Input Alignment
Archives and mailing list
subscription details can be found in the Jalview web site's \href{http://www.jalview.org/community}{community section}.
+
\section{Navigation}
\label{jvnavigation}
The major features of the Jalview Desktop are illustrated in Figure \ref{anatomy}. The alignment window is the primary window for editing and visualization, and can contain several independent views of the alignment being worked with. The other windows (Trees, Structures, PCA plots, etc) are linked to a specific alignment view. Each area of the alignment window has a separate context menu accessed by clicking the right mouse button.
Jalview has two navigation and editing modes: {\bf normal mode}, where
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 may often need to type {\bf function
- [Fn] key with F2 key}
- [Fn]-F2.
+ is used to switch between these two modes.
+
+ {\em Note:} On MacBooks and other laptops with compact keyboards, you may need
+ to press the {\bf function key [Fn]} when pressing any of the numbered function
+ keys. So to toggle between keyboard and normal mode, press [Fn]-[F2].
+
\begin{figure}[htb]
\begin{center}
Gaps can be removed by dragging the residue to the immediate right of the gap
leftwards whilst holding down [SHIFT] (for single sequences) or [CTRL] (for a group of sequences).
-\subsection{Sliding Sequences}
-Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
-sequences are selected will ``slide'' the entire selected sequences to the left
-or right (respectively). Slides occur regardless of the region selection -
-which, for example, allows you to easily reposition misaligned subfamilies
-within a larger alignment.
-% % better idea to introduce hiding sequences, and use the invert selection, hide
-% others, to simplify manual alignment construction
-
-\subsection{Editing in Cursor mode}
-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]
-or [SHIFT]-[SPACE] (both keys held down together).
-
-Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
-have everything unselected by pressing ESC. The gap under the cursor will be
-removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
-will be deleted up to the number specified. To delete gaps from all sequences of
-a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
-together). Note that the deletion will only occur if the gaps are in the same
-columns in all sequences in the selected group, and those columns are to the
-right of the selected residue.
-
\newpage
\exercise{Editing Alignments}
backwards and replay the edits you have made.}
}
+\subsection{Sliding Sequences}
+Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
+sequences are selected will ``slide'' the entire selected sequences to the left
+or right (respectively). Slides occur regardless of the region selection -
+which, for example, allows you to easily reposition misaligned subfamilies
+within a larger alignment.
+% % better idea to introduce hiding sequences, and use the invert selection, hide
+% others, to simplify manual alignment construction
+
+\subsection{Editing in Cursor mode}
+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]
+or [SHIFT]-[SPACE] (both keys held down together).
+
+Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
+have everything unselected by pressing ESC. The gap under the cursor will be
+removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
+will be deleted up to the number specified. To delete gaps from all sequences of
+a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
+together). Note that the deletion will only occur if the gaps are in the same
+columns in all sequences in the selected group, and those columns are to the
+right of the selected residue.
+
\exercise{Keyboard Edits}
{This continues on from the previous exercise, and recreates the final part of the example ferredoxin
} \parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_rnahelix.pdf} }
+\subsubsection{User Defined}
+This dialog allows the user to create any number of named colour schemes at
+will. Any residue may be assigned any colour. The colour scheme can then be
+named. If you save the colour scheme, this name will appear on the Colour menu
+(Figure \ref{usercol}).
+
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2.5in]{images/col_user1.pdf}
+\includegraphics[width=2in]{images/col_user2.pdf}
+\includegraphics[width=1.75in]{images/col_user3.pdf}
+\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).}
+\label{usercol}
+\end{center}
+\end{figure}
+
\exercise{Colouring Alignments}{
\label{color}
Note: Before you begin this exercise, ensure that the {\sl Apply Colour
{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
-\subsubsection{User Defined}
-This dialog allows the user to create any number of named colour schemes at
-will. Any residue may be assigned any colour. The colour scheme can then be
-named. If you save the colour scheme, this name will appear on the Colour menu
-(Figure \ref{usercol}).
-
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2.5in]{images/col_user1.pdf}
-\includegraphics[width=2in]{images/col_user2.pdf}
-\includegraphics[width=1.75in]{images/col_user3.pdf}
-\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).}
-\label{usercol}
-\end{center}
-\end{figure}
-
\exercise{User Defined Colour Schemes}{
\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialog window will open.}
will be performed for all selected sequences. After this is done, you can see
the added database references in a tool tip by mousing over the sequence
ID\footnote{Tip:
-The sequence ID tooltip can often become large for heavily cross referenced sequence IDs. Use the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ }
-submenu to disable the display of database cross references or non-positional
-features. }, now shows the Uniprot ID and any associated PDB structures.
+If sequence ID tooltip obscures your view, then use the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ }
+submenu option to disable the display of database cross references or non-positional
+features. }, now shows the Uniprot ID and any associated PDB structures.
%
% \begin{figure}[htbp]
% \begin{center}
views that colour different areas or domains of the alignment. This option is
further explored in Section \ref{complexstructurecolours}.
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=5.5in]{images/mviewstructurecol.pdf}
-\caption{{\bf Choosing a different view for colouring a structure display}
-Browsing the {\sl View $\Rightarrow$ Colour by ..} menu provides full control
-of which alignment view is used to colour structures when the {\sl Colours
-$\Rightarrow$ By Sequence} option is selected.}
-\label{mviewstructurecol}
-\end{center}
-\end{figure}
\exercise{Aligning Structures using the Ferredoxin
Sequence Alignment}{\label{superpositionex}
Which view do you think give the best 3D superposition, and why ?} }
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5.5in]{images/mviewstructurecol.pdf}
+\caption{{\bf Choosing a different view for colouring a structure display}
+Browsing the {\sl View $\Rightarrow$ Colour by ..} menu provides full control
+of which alignment view is used to colour structures when the {\sl Colours
+$\Rightarrow$ By Sequence} option is selected.}
+\label{mviewstructurecol}
+\end{center}
+\end{figure}
+
\subsubsection{Colouring Complexes}
\label{complexstructurecolours}
The ability to control which multiple alignment view is used to colour
\begin{center}
\includegraphics[width=2.25in]{images/jpred1.pdf}
\includegraphics[width=3in]{images/jpred2.pdf}
-\caption{{\bf Secondary Structure Prediction} Status (left) and results (right) windows for JNet predictions. }
+\caption{{\bf Secondary Structure Prediction} Status (left) and results (right)
+windows for JPred predictions. }
\label{jpred}
\end{center}
\end{figure}
predictions are included as annotations. Consult the Jpred documentation for
information on interpreting these results.
-\subsection{Hidden Columns and JNet Predictions}
+\subsection{Hidden Columns and JPred Predictions}
\label{hcoljnet}
Hidden columns can be used to exclude parts of a sequence or profile from the
input sent to the JNet service. For instance, if a sequence is known to include
{\bf Homework:} Go back to the last step of exercise \ref{annotatingalignex} and
follow the instructions to view the Jalview annotations file created from the annotations
-generated by the JPred server for your sequence.
-
-}
-
+generated by the JPred server for your sequence.}
\section{Protein Disorder Prediction}
\label{protdisorderpred}
allows access to protein disorder prediction services provided by the configured
JABAWS servers.
-
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5in]{images/disorderpredannot.pdf}
\end{center}
\end{figure}
-
\subsection{Disorder Prediction Results}
Each service operates on sequences in the alignment to identify regions likely
to be unstructured or flexible, or alternately, fold to form globular domains.
thresholding (described in Section \ref{featureschemes}) can be used to
highlight differences in disorder prediction across aligned sequences.
-
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5in]{images/disorderpred.pdf}
the associated sequence in the alignment display, and double clicking will
select that sequence.
-
\subsection{Disorder Predictors provided by JABAWS 2.0}
For full details of each predictor and the results that Jalview can display,
please consult
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
+\exstep{Apply the IUPred disorder prediction method. 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.
-
-{\sl Note how well the regions predicted to be disordered by the methods agree
-with the structure.}
-}
-
-}
+the sequences by the long and short disorder predictors. {\sl Note how well the disordered regions predicted by each method agree
+with the structure.}}}
\chapter{DNA and RNA Sequences}
\label{dnarna}
\subsection{Running your own JABA Server}
You can download and run JABA on your own machine using the `VMWare' or
-VirtualBox virtual machine environments. If you would like to learn how to do
+VirtualBox virtual machine environments. If you would like to do
this, there are full instructions at the
\href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}.
WARNING: This is large (about 300MB) and will take some time to download.
}
\exstep{Unpack the archive's contents to a place on your machine with at least
-2GB of free space.
-
-(On Windows, right click on the archive, and use the 'Extract archive..' option).
+2GB of free space (On Windows, right click on the archive, and use the 'Extract
+archive..' option).
}
\exstep{Open the newly extracted directory and double click the VMWare virtual
machine configuration file (jabaws.vcf). This will launch the VMWare player.