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}
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}
\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
+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}
\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 do
-this, There are full instructions at the
+this, there are full instructions at the
\href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}.
\exercise{Installing a JABA Virtual Machine on your Computer}{
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
+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
git://source.jalview.org / jalview-manual.git / commitdiff