-\subsection{Customising the Parameters used for Alignment}
-
-JABA web services allow you to vary the parameters used when performing a
-bioinformatics analysis. For JABA alignment services, this means you are
-usually able to modify the following types of parameters:
-\begin{list}{$\bullet$}{}
-\item Amino acid or nucleotide substitution score matrix
-\item Gap opening and widening penalties
-\item Types of distance metric used to construct guide trees
-\item Number of rounds of re-alignment or alignment optimisation
-\end{list}
-
-
-\subsubsection{Getting Help on the Parameters for a Service}
-Each parameter available for a method usually has a short description, which
-Jalview will display as a tooltip, or as a text pane that can be opened under
-the parameter's controls. In the parameter shown in Figure
-\ref{clustalwparamdetail}, the description was opened by selecting the button on the left hand side. Online help for the
-service can also be accessed, by right clicking the button and selecting a URL
-from the pop-up menu that will open.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2.5in]{images/clustalwparamdetail.pdf}
-\caption{{\bf ClustalW parameter slider detail}. From the ClustalW {\sl Clustal $\Rightarrow$ Edit settings and run ...} dialog box. }
-\label{clustalwparamdetail}
-\end{center}
-\end{figure}
-
-\subsection{Alignment Presets}
-The different multiple alignment algorithms available from JABA vary greatly in
-the number of adjustable parameters, and it is often difficult to identify what
-are the best values for the sequences that you are trying to align. For these
-reasons, each JABA service may provide one or more presets -- which are
-pre-defined sets of parameters suited for particular types of alignment
-problem. For instance, the Muscle service provides the following presets:
-\begin{list}{$\bullet$}{}
-\item Large alignments (balanced)
-\item Protein alignments (fastest speed)
-\item Nucleotide alignments (fastest speed)
-\end{list}
-
-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 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.
-
-\subsubsection{Alignment Service Limits}
-Multiple alignment is a computationally intensive calculation. Some JABA server
-services and service presets only allow a certain number of sequences to be
-aligned. The precise number will depend on the server that you are using to
-perform the alignment. Should you try to submit more sequences than a service
-can handle, then an error message will be shown informing you of the maximum
-number allowed by the server.
-
-\subsection{User Defined Presets}
-Jalview allows you to create your own presets for a particular service. To do
-this, select the `{\sl Edit settings and run ...}' option for your service,
-which will open a parameter editing dialog box like the one shown in Figure
-\ref{jwsparamsdialog}.
-
-The top row of this dialog allows you to browse the existing presets, and
-when editing a parameter set, allows you to change its nickname. As you
-adjust settings, buttons will appear at the top of the parameters dialog that
-allow you to Revert or Update the currently selected user preset with your changes, Delete the current preset, or Create a new preset, if none exists with the given name. In addition to the parameter set name, you can also provide a short
-description for the parameter set, which will be shown in the tooltip for the
-parameter set's entry in the web services menu.
-
-\begin{figure}[htbc]
-\center{
-\includegraphics[width=3in]{images/jvaliwsparamsbox.pdf}
-\caption{{\bf Jalview's JABA alignment service parameter editing dialog box}.}
-\label{jwsparamsdialog} }
-\end{figure}
-
-\subsubsection{Saving Parameter Sets}
-When creating a custom parameter set, you will be asked for a file name to save
-it. The location of the file is recorded in the Jalview user preferences in the
-same way as a custom alignment colourscheme, so when Jalview is launched again,
-it will show your custom preset amongst the options available for running the
-JABA service.
-
-%
-% \exercise{Creating and using user defined presets}{\label{createandusepreseex}
-% \exstep{Import the file at
-% \textsf{http://www.jalview.org/tutorial/fdx\_unaligned.fa} into jalview.}
-% \exstep{Use the `{\slDiscover Database Ids}' function to recover the PDB cross
-% references for the sequences.}
-% \exstep{Align the sequences using the default ClustalW parameters.}
-% \exstep{Use the `{\sl Edit and run..}'
-% option to open the ClustalW parameters dialog box, and create a new preset using
-% the following settings:
-% \begin{list}{$\bullet$}{}
-% \item BLOSUM matrix (unchanged)
-% \item Gap Opening and End Gap penalties = 0.05
-% \item Gap Extension and Separation penalties = 0.05
-% \end{list}
-%
-% As you edit the parameters, buttons will appear on the dialog box
-% allowing you revert your changes or save your settings as a new parameter
-% set.
-%
-% Before you save your settings, remeber to give them a meaningful name by editing
-% the text box at the top of the dialog box.
-% }
-% \exstep{Repeat the alignment using your new parameter set by selecting it from
-% the {\sl ClustalW Presets menu}.}
-% \exstep{These sequences have PDB structures associated with them, so it is
-% possible to compare the quality of the alignments.
-%
-% Use the {\sl View all {\bf N}
-% structures} option to calculate the superposition of 1fdn on 1fxd for both
-% alignments (refer to section \ref{superposestructs} for instructions). Which
-% alignment gives the best RMSD ? }
-% \exstep{Apply the same alignment parameter settings to the example alignment
-% (available from \textsf{http://www.jalview.org/examples/uniref50.fa}).
-%
-% Are there differences ? If not, why not ?
-% }
-% }
-
-\section{Protein Alignment Conservation Analysis}
-\label{aacons}
-The {\sl Web Service $\Rightarrow$ Conservation} menu controls the computation
-of up to 17 different amino acid conservation measures for the current alignment
-view. The JABAWS AACon Alignment Conservation Calculation Service, which is used
-to calculate these scores, provides a variety of standard measures described by
-Valdar in 2002\footnote{Scoring residue conservation. Valdar (2002) {\sl
-Proteins: Structure, Function, and Genetics} {\bf 43} 227-241.} as well as an efficient implementation of the SMERFs
-score developed by Manning et al. in 2008.\footnote{SMERFS Score Manning et al. {\sl BMC
-Bioinformatics} 2008, {\bf 9} 51 \href{http://dx.doi.org/10.1186/1471-2105-9-51}{doi:10.1186/1471-2105-9-51}}
-
-\subsubsection{Enabling and Disabling AACon Calculations}
-When the AACon Calculation entry in the {\sl Web Services $\Rightarrow$
-Conservation} menu is ticked, AACon calculations will be performed every time
-the alignment is modified. Selecting the menu item will enable or disable
-automatic recalculation.
-
-\subsubsection{Configuring which AACon Calculations are Performed}
-The {\sl Web Services $\Rightarrow$ Conservation $\Rightarrow$ Change AACon
-Settings ...} menu entry will open a web services parameter dialog for the
-currently configured AACon server. Standard presets are provided for quick and
-more expensive conservation calculations, and parameters are also provided to
-change the way that SMERFS calculations are performed.
-AACon settings for an alignment are saved in Jalview projects along with the
-latest calculation results.
-
-\subsubsection{Changing the Server used for AACon Calculations}
-If you are working with alignments too large to analyse with the public JABAWS
-server, then you will most likely have already configured additional JABAWS
-servers. By default, Jalview will chose the first AACon service available from
-the list of JABAWS servers available. If available, you can switch to use
-another AACon service by selecting it from the {\sl Web Services $\Rightarrow$
-Conservation $\Rightarrow$ Switch Server} submenu.
-
-% TODO
-\section{Protein Secondary Structure Prediction}
-\label{protsspredservices}
-Protein secondary structure prediction is performed using the
-Jpred\footnote{{\sl ``The Jpred 3 Secondary Structure Prediction Server''} Cole, C., Barber, J. D. and Barton, G. J. (2008) {\sl Nucleic Acids Research} {\bf 36}, (Web Server Issue) W197-W201
-
-{\sl ``Jpred: A Consensus Secondary Structure Prediction Server''} Cuff, J. A.,
-Clamp, M. E., Siddiqui, A. S., Finlay, M. and Barton, G. J. (1998) {\sl
-Bioinformatics} {\bf 14}, 892-893} server at the University of
-Dundee\footnote{http://www.compbio.dundee.ac.uk/www-jpred/}. The behaviour of
-this calculation depends on the current selection:
-\begin{list}{$\circ$}{}
-\item If nothing is selected, Jalview will check the length of each alignment row to determine if the visible sequences in the view are aligned.
-\begin{list}{-}{}
- \item If all rows are the same length (often due to the
- application of the {\sl Edit $\Rightarrow$ Pad Gaps} option), then
- a JPred prediction will be run for the first sequence in the
- alignment, using the current alignment as the profile to use for prediction.
- \item Otherwise, just the first sequence will be submitted for a
- full JPred prediction.
-\end{list}
-\item If just one sequence (or a region in one sequence) has been selected, it
-will be submitted to the automatic JPred prediction server for homolog detection
-and prediction.
-\item If a set of sequences are selected, and they appear to be aligned using
-the same criteria as above, then the alignment will be used for a JPred
-prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
-\end{list}
-Jpred is launched in the same way as the other web services. Select {\sl Web
-Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
-Secondary Structure Prediction}\footnote{JNet is the Neural Network based
-secondary structure prediction method that the JPred server uses.} from the
-alignment window menu (Figure \ref{jpred}).
-A status window opens to inform you of the progress of the job. Upon completion, a new alignment window opens and the Jpred
-predictions are included as annotations. Consult the Jpred documentation for
-information on interpreting these results.
-
-\begin{figure}[htbp]
-\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. }
-\label{jpred}
-\end{center}
-\end{figure}