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.}
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
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 regions predicted to be disordered by the methods 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
-this, there are full instructions at the
+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}.
\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 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.
git://source.jalview.org / jalview-manual.git / commitdiff