-\exercise{Aligning Structures using the Ferredoxin
-Sequence Alignment}{\label{superpositionex}
-
-\exstep{Continue with the Jalview project created in exercise
-\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
-IDs associated with the FER1\_MAIZE sequence.}
-\exstep{Once discovery has completed, use the {\sl
-View PDB Structure} submenu to view the PDB file associated with FER1\_MAIZE.
-Jalview will give you the option of aligning the structure to the one already
-open. To superimpose the structure associated with FER1\_MAIZE with the one
-associated with FER1\_SPIOL, press the {\bf Yes} button.
-
-{\sl The Jmol view will update to show both structures, and one will be
-moved on to the other. If this doesn't happen, use the Align function in the Jmol submenu}}
-\exstep{Create a new view on the alignment, and hide all but columns 121
-through to 132.}
-\exstep{Use the {\sl Jmol} submenu to
-recompute the superposition using just columns 121-132 of the alignment.
-
-{\sl Note how the molecules shift position when superposed using a short part of
-the two structures.}}
-\exstep{Compare the initial and final RMSDs for superimposing molecules with
-the small section and with the whole alignment. Which view do you think give the
-best 3D superposition, and why ?} }
-
-\subsection{Colouring Structure Data Associated with Multiple Alignments and
-Views} Normally, the original view from which a particular structure view was
-opened will be the one used to colour structure data. If alignments involving
-sequences associated with structure data shown in a Jmol have multiple views, Jalview gives you full control
-over which alignment, or alignment view, is used to colour the structure
-display. Sequence-structure colouring associations are
-changed {\sl via} the {\sl View $\Rightarrow$ Colour by ..} menu, which lists all
-views associated with data shown in the embedded Jmol view. A tick is shown beside
-views currently used as colouring source, and moving the
-mouse over each view will bring it to the front of the alignment display,
-allowing you to browse available colour sources prior to selecting one. If the
-{\sl Select many views} option is selected, then multiple views can be selected as sources for colouring the
-structure data. {\sl Invert selection} and {\sl Select all views} options are also provided to quickly change between multi-view selections.
-
-Note that the {\sl Select many views} option is useful if you have different
-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}
-
-\subsubsection{Colouring Complexes}
-\label{complexstructurecolours}
-The ability to control which multiple alignment view is used to colour
-structural data is essential when working with data relating to
-multidomain biomolecules and complexes.
-
-In these situations, each chain identified in the structure may have a different
-evolutionary history, and a complete picture of functional variation can
-only be gained by integrating data from different alignments on the same
-structure view. An example of this is shown in Figure
-\ref{mviewalcomplex}, based on data from Song et. al.\footnote{Structure of
-DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation. Jikui Song, Olga Rechkoblit, Timothy H. Bestor, and Dinshaw J. Patel.
-{\sl Science} 2011 {\bf 331} 1036-1040
-\href{http://www.sciencemag.org/content/331/6020/1036}{DOI:10.1126/science.1195380}}
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[]{images/mchainstructureview.pdf}
-\caption{{\bf The biological assembly of Mouse DNA Methyltransferase-1 coloured
-by Pfam alignments for its major domains} Alignments for each domain within the
-Uniprot sequence DNMT1\_MOUSE have been used to visualise sequence conservation
-in each component of this protein-DNA complex. Instructions for recreating this figure are given in exercise \ref{dnmtcomplexex}. }
-\label{mviewalcomplex}
-\end{center}
-\end{figure}
-
-\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.}
-
-\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/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
-step 1 onto one of the alignments to associate it with the mouse sequence in
-that Pfam domain family.}
-\exstep{For every DNMT1\_MOUSE sequence in the alignment, use the sequence
-ID popup menu's {\sl Structure} submenu to view the DNMT1\_MOUSE structure for the associated mouse sequence. When given the option, {\bf view all of the structures in the same Jmol viewer}. Check the contents of the {\sl View $\Rightarrow$ Colour by ..} submenu to see what alignments can be used to
-colour the sequence.}
-\exstep{Repeat the previous two steps for each of
-the other alignments. In each case, when performing the `View DNMT1\_MOUSE.pdb'
-step, Jalview will ask if you wish to create a new Jmol view. You should
-respond `No', {\bf ensuring that each sequence fragment is associated with the same Jmol view}.}
-\exstep{Pick a different colourscheme for each alignment, and use the {\sl
-Colour by ..} submenu to ensure they are all used to colour the complex shown
-in the Jmol window.}
-\exstep{The final step needed to reproduce the shading in Figure
-\ref{mviewalcomplex} is to use the {\sl Colour $\Rightarrow$ By
-Annotation } option in each alignment window to shade the alignment by the
-{\bf Conservation} annotation row. This function was described in section
-\ref{colourbyannotation}.
-
-Ensure that you first disable the {\sl View $\Rightarrow$ Show Features} menu option, or you may not see any colour changes in the associated structure.
-
-{\sl Note: Choose a different shading scheme for each
-alignment so that the regions of strong physicochemical conservation are highlighted. This
-kind of shading will reveal conserved regions of interaction between domains
-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).}
-}
-
-\section{Analysis of Alignments}
-\label{alignanalysis}
-Jalview provides support for sequence analysis in two ways. A number of
-analytical methods are `built-in', these are accessed from the {\sl Calculate}
-alignment window menu. Computationally intensive analyses are run outside
-Jalview {\sl via} web services - these are typically accessed {\sl via} the {\sl
-Web Service} menu, and described in \ref{jvwebservices} and subsequent sections.
-In this section, we describe the built-in analysis capabilities common to both
-the Jalview Desktop and the JalviewLite applet.
-
-\subsection{PCA}
-This calculation creates a spatial representation of the similarities within the
-current selection or the whole alignment if no selection has been made. After
-the calculation finishes, a 3D viewer displays the each sequence as a point in
-3D `similarity space'. Sets of similar sequences tend to lie near each other in
-this space.
-Note: The calculation is computationally expensive, and may fail for very large
-sets of sequences - because the JVM has run out of memory. Memory issues, and
-how to overcome them, were discussed in Section \ref{memorylimits}.
-
-\subsubsection{What is PCA?}
-Principal components analysis is a technique for examining the structure of
-complex data sets. The components are a set of dimensions formed from the
-measured values in the data set, and the principle component is the one with the
-greatest magnitude, or length. The sets of measurements that differ the most
-should lie at either end of this principle axis, and the other axes correspond
-to less extreme patterns of variation in the data set.
-In this case, the components are generated by an eigenvector decomposition of
-the matrix formed from the sum of pairwise substitution scores at each aligned
-position between each pair of sequences. The basic method is described in the
-1995 paper by {\sl G. Casari, C. Sander} and {\sl A. Valencia} \footnote{{\sl
-Nature Structural Biology} (1995) {\bf 2}, 171-8.
-PMID: 7749921} and implemented at the SeqSpace server at the EBI.
-
-Jalview provides two different options for the PCA calculation. Protein PCAs are
-by default computed using BLOSUM 62 pairwise substitution scores, and nucleic
-acid alignment PCAs are computed using a score model based on the identity
-matrix that also treats Us and Ts as identical, to support analysis of both RNA
-and DNA alignments. The {\sl Change Parameters} menu also allows the calculation
-method to be toggled between SeqSpace and a variant calculation that is detailed
-in Jalview's built in documentation.\footnote{See
-\url{http://www.jalview.org/help/html/calculations/pca.html}.}
-
-\subsubsection{The PCA Viewer}
-
-PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principle
-Component Analysis} menu option. {\bf PCA requires a selection containing at
-least 4 sequences}. A window opens containing the PCA tool (Figure \ref{PCA}).
-Each sequence is represented by a small square, coloured by the background
-colour of the sequence ID label. The axes can be rotated by clicking and
-dragging the left mouse button and zoomed using the $\uparrow$ and $\downarrow$
-keys or the scroll wheel of the mouse (if available). A tool tip appears if the
-cursor is placed over a sequence. Sequences can be selected by clicking on them.
-[CTRL]-Click can be used to select multiple sequences.
-\begin{figure}[hbtp]
-\begin{center}
-\includegraphics[width=2in]{images/PCA1.pdf}
-\includegraphics[width=3in]{images/PCA3.pdf}
-\caption{{\bf PCA Analysis.} }
-\label{PCA}
-\end{center}
-\end{figure}
-
-Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$
-Show Labels} menu option, and the plot background colour changed {\sl via} the
-{\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical
-representation of the PCA plot can be exported as an EPS or PNG image {\sl via}
-the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
-
-\exercise{Principle Component Analysis}{ \exstep{Load the alignment at
-\textsf{http://www.jalview.org/examples/exampleFile.jar} and press [ESC] to clear any selections. Alternatively, select {\sl Select $\Rightarrow$ Undefine Groups} to remove all groups and colourschemes. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
-\exstep{ Click on the tree window. Careful selection of the tree partition
-location will divide the alignment into a number of groups, each of a different
-colour. Note how the colour of the sequence ID label matches both the colour of
-the partitioned tree and the points in the PCA plot.
-} }
-
-\subsubsection{PCA Data Export}
-Although the PCA viewer supports export of the current view, the plots produced
-are rarely suitable for direct publication. The PCA viewer's {\sl File} menu
-includes a number of options for exporting the PCA matrix and transformed points
-as comma separated value (CSV) files. These files can be imported by tools such
-as {\bf R} or {\bf gnuplot} in order to graph the data.
-
-\subsection{Trees}
-\label{trees}
-Jalview can calculate and display trees, providing interactive tree-based
-grouping of sequences though a tree viewer. All trees are calculated {\sl via}
-the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu.
-Trees can be calculated from distance matrices determined from \% identity or
-aggregate BLOSUM 62 score using either {\sl Average Distance} (UPGMA) or {\sl
-Neighbour Joining} algorithms. The input data for a tree is either the selected
-region or the whole alignment, excluding any hidden regions.
-
-On calculating a tree, a new window opens (Figure \ref{trees1}) which contains
-the tree. Various display settings can be found in the tree window {\sl View}
-menu, including font, scaling and label display options, and the {\sl File
-$\Rightarrow$ Save As} submenu contains options for image and Newick file
-export. Newick format is a standard file format for trees which allows them to
-be exported to other programs. Jalview can also read in external trees in
-Newick format {\sl via} the {\sl File $\Rightarrow$ Load Associated Tree} menu
-option. Leaf names on imported trees will be matched to the associated alignment
-- unmatched leaves will still be displayed, and can be highlighted using the
-{\sl View $\Rightarrow$ Mark Unlinked Leaves} menu option.
-
-
-\begin{figure}
-\begin{center}
-\includegraphics[width=2.5in]{images/trees1.pdf}
-\includegraphics[width=2.5in]{images/trees2.pdf}
-\includegraphics[width=1.25in]{images/trees4.pdf}
-\caption{{\bf Calculating Trees} Jalview provides four built in models for calculating trees.
-Jalview can also load precalculated trees in Newick format (right).}
-\label{trees1}
-\end{center}
-\end{figure}
-
-
-Clicking on the tree brings up a cursor across the height of the tree. The
-sequences are automatically partitioned and coloured (Figure \ref{trees2}). To
-group them together, select the {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$
-By Tree Order $\Rightarrow$ \ldots} alignment window menu option and choose the
-correct tree. The sequences will then be sorted according to the leaf order
-currently shown in the tree view. The coloured background to the sequence IDs
-can be removed with {\sl Select $\Rightarrow$ Undefine Groups} from the
-alignment window menu. Note that tree partitioning will also remove any groups
-and colourschemes on a view, so create a new view ([CTRL-T]) if you wish to
-preserve these.
-
-\begin{figure}
-\begin{center}
-\includegraphics[width=5in]{images/trees3.pdf}
-\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate
-groups in Jalview.}
-\label{trees2}
-\end{center}
-\end{figure}
-
-%\subsubsection{Multiple Views and Input Data recovery from PCA and Tree Viewers}
-% move to ch. 3 ?
-%Both PCA and Tree viewers are linked analysis windows. This means that their selection and display are linked to a particular alignment, and control and reflect the selection state for a particular view.
-
-\subsubsection{Recovering input Data for a Tree or PCA Plot Calculation}
-\parbox[c]{5in}{
-The {\sl File $\Rightarrow$ Input Data } option will open a new alignment window containing the original data used to calculate the tree or PCA plot (if available). This function is useful when a tree has been created and then the alignment subsequently changed.
-}
-\parbox[c]{1.25in}{\centerline{\includegraphics[width=1.25in]{images/pca_fmenu.pdf}
-}}
-
-\subsubsection{Changing the associated View for a Tree or PCA Viewer}
-\parbox[c]{4in}{
-The {\sl View $\Rightarrow$ Associated Nodes With $\Rightarrow$ .. } submenu is shown when the viewer is associated with an alignment that is involved in multiple views. Selecting a different view does not affect the tree or PCA data, but will change the colouring and display of selected sequences in the display according to the colouring and selection state of the newly associated view.
-} \parbox[c]{3in}{\centerline{
-\includegraphics[width=2.5in]{images/pca_vmenu.pdf} }}
-
-
-\exercise{Trees}{
-\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.}
-\exstep{Select from sequence 2 column 60 to sequence 12 column 123. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear. It can be seen that the tree contains 11 sequences. It has been coloured according to the already selected groups from the first tree and is calculated purely from the residues in the selection.
-Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the alignment for the calculation of trees.
-}
-\exstep{Recover the {\sl Input Data} for the tree you just calculated from the {\sl File} menu. Check the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the alignment. Now select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}.
-
-A warning dialog box {\bf ``Sequences not aligned'' } appears because the sequences input to the tree calculation are of different lengths. }
-
-\exstep{Now select {\sl Edit $\Rightarrow$ Pad Gaps } and try to perform the tree calculation again - this time a new tree should appear.
-
-This demonstrates the use of the {\sl Pad Gaps } editing preference, which ensures that all sequences are the same length after editing. }
-
-}
-
-\subsection{Tree Based Conservation Analysis}
-\label{treeconsanaly}
-
-Trees reflect the pattern of global sequence similarity exhibited by the
-alignment, or region within the alignment, that was used for their calculation.
-The Jalview tree viewer enables sequences to be partitioned into groups based
-on the tree. This is done by clicking within the tree viewer window. Once subdivided, the
-conservation between and within groups can be visually compared in order to
-better understand the pattern of similarity revealed by the tree and the
-variation within the clades partitioned by the grouping. The conservation based
-colourschemes and the group associated conservation and consensus annotation
-(enabled using the alignment window's {\sl View $\Rightarrow$ Autocalculated
-Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
-can help when working with larger alignments.
-
-\exercise{Tree Based Conservation Analysis}{
-\label{consanalyexerc}
-\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
-\exstep{Build a Neighbourjoining tree using BLOSUM62 and use the {\sl Sort Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.}
-\exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
-
-You may find it easier to browse the alignment if you first uncheck the {\sl View $\Rightarrow$ Show Annotations} option, and open the Overview Window to aid navigation.}
-\exstep{Try changing the colourscheme to BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected)}
-{\sl Note: You may want to save the alignment and tree as a project file, since
-it is used in the next few exercises. } }
-
-\subsection{Redundancy Removal}
-
-The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function, but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater than the current threshold are highlighted in black. The [Remove] button can then be used to delete these sequences from the alignment as an edit operation\footnote{Which can usually be undone. A future version of Jalview may allow redundant sequences to be hidden, or represented by a chosen sequence, rather than deleted.}.
-\begin{figure}
-\begin{center}
-\includegraphics[width=5.5in]{images/redundancy.pdf}
-\end{center}
-\label{removeredundancydialog}
-\caption{The Redundancy Removal dialog box opened from the edit menu. Sequences that exceed the current percentage identity threshold and are to be removed are highlighted in black.}
-\end{figure}
-
-\exercise{Remove Redundant Sequences}{
-
-\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.}
-\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Mark Unlinked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
-\exstep{Use the [Undo] button on the dialog to recover the sequences. Note that the * symbols disappear from the tree display.}
-\exstep{Experiment with the redundancy removal and observe the relationship between the percentage identity threshold and the pattern of unlinked nodes in the tree display.}
-}
-
-\subsection{Subdividing the Alignment According to Specific Mutations}
-
-It is often necessary to explore variations in an alignment that may correlate
-with mutations observed in a particular region; for example, sites exhibiting
-single nucleotide polymorphism, or residues involved in substrate recognition in
-an enzyme. One way to do this would be to calculate a tree using the specific
-region, and subdivide it in order to partition the alignment.
-However, calculating a tree can be slow for large alignments, and the tree may
-be difficult to partition when complex mutation patterns are being analysed. The
-{\sl Select $\Rightarrow$ Make groups for selection } function was introduced to
-make this kind of analysis easier. When selected, it will use the characters in
-the currently selected region to subdivide the alignment. For example, if a
-single column is selected, then the alignment (or each group defined on the
-alignment) will be divided into groups based on the residue or nucleotide found
-at that position. These new groups are annotated with the characters in the
-selected region, and Jalview's group based conservation analysis annotation and
-colourschemes can then be used to reveal any associated pattern of sequence
-variation across the whole alignment.
-
-\subsection{Automated Annotation of Alignments and Groups}
-
-On loading a sequence alignment, Jalview will normally\footnote{Automatic
-annotation can be turned off in the {\sl Visual } tab in the {\sl Tools
-$\Rightarrow$ Preferences } dialog box.} calculate a set of automatic annotation
-rows which are shown below the alignment. For nucleotide sequence alignments,
-only an alignment consensus row will be shown, but for amino acid sequences,
-alignment quality (based on BLOSUM 62) and physicochemical conservation will
-also be shown. Conservation is calculated according to Livingstone and
-Barton\footnote{{\sl ``Protein Sequence Alignments: A Strategy for the
-Hierarchical Analysis of Residue Conservation." } Livingstone C.D. and Barton
-G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}.
-Consensus is the modal residue (or {\tt +} where there is an equal top residue).
-The inclusion of gaps in the consensus calculation can be toggled by
-right-clicking on the the Consensus label and selecting {\sl Ignore Gaps in
-Consensus} from the context menu. Quality is a measure of the inverse likelihood
-of unfavourable mutations in the alignment. Further details on these
-calculations can be found in the on-line documentation.
-
-These annotations can be hidden and deleted but are only created on loading an
-alignment. If they are deleted then the alignment should be saved and reloaded
-to restore them. Jalview provides a toggle to autocalculate a consensus sequence
-upon editing. This is normally selected by default, but can be turned off for
-large alignments {\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
-Consensus} menu option if the interface is too slow.
-
-\subsubsection{Group Associated Annotation}
-\label{groupassocannotation}
-Group associated consensus and conservation annotation rows reflect the
-sequence variation within a particular group. Their calculation is enabled
-by selecting the {\sl Group Conservation} or {\sl Group Consensus} options in
-the {\sl View $\Rightarrow$ Autocalculated Annotation } submenu of the alignment
-window.
-
-\subsubsection{Alignment and Group Sequence Logos}
-\label{seqlogos}
-
-The consensus annotation row that is shown below the alignment can be overlaid
-with a sequence logo that reflects the symbol distribution at each column of
-the alignment. Right click on the Consensus annotation row and select the {\sl Show
-Logo} option to display the Consensus profile for the group or alignment.
-Sequence logos can be enabled by default for all new alignments {\sl via} the
-Visual tab in the Jalview desktop's preferences dialog box.
-
-\exercise{Group Conservation Analysis}{
-\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
-\exstep{Create a new view, and ensure the annotation panel is displayed, and
-enable the display of {\sl Group Consensus} and the display of sequence
-logos to make it easier to see the different residue populations within each group.}
-\exstep{Select a column exhibiting about 50\% conservation that lies within the
-central conserved region of the alignment. Subdivide the alignment according to
-this selection using {\sl Select $\Rightarrow$ Make groups for selection}.}
-\exstep{Re-order the alignment according to the new groups that have been
-defined. Click on the group annotation row IDs to select groups exhibiting a
-specific mutation.}
-\exstep{Select another column exhibiting about 50\% conservation
-overall, and subdivide the alignment further. Note that the new groups
-inherit the names of the original groups, allowing you to identify the
-combination of mutations that resulted in the subdivision.
-}
-\exstep{Clear the groups, and try to subdivide the alignment using two
-non-adjacent columns.
-
-{\sl Hint: You may need to hide the intervening columns before you can select
-both of the columns that you wish to use to subdivide the alignment.}}
-\exstep{Switch back to the original view, and experiment with subdividing
-the tree groups made in the previous exercise.}
-}
-
-\subsection{Other Calculations}
-
-
-\subsubsection{Pairwise Alignments}
-
-Jalview can calculate optimal pairwise alignments between arbitrary sequences {\sl via} the {\sl Calculate $\Rightarrow$ Pairwise Alignments\ldots} menu option. Global alignments of all pairwise combinations of the selected sequences are performed and the results returned in a text box.
-
-\begin{figure}[]
-\begin{center}
-\includegraphics[width=4in]{images/pairwise.pdf}
-\caption{{\bf Pairwise alignment of sequences.} Pairwise alignments of three selected sequences are shown in a textbox.}
-\label{pairwise}
-\end{center}
-\end{figure}
-
-\pagebreak[2]
-
-\section{Webservices}
-\label{jvwebservices}
-The term ``Webservices'' refers to a variety of data exchange
-mechanisms based on HTTP.\footnote{HTTP: Hyper-Text Transfer Protocol.}
-
-\parbox[c]{4.5in}{Jalview can exploit public webservices to access databases
-remotely, and also submit data to public services by opening pages with your web browser. These types of
-services are `one-way', {\sl i.e.} data is either sent to the webservice or
-retrieved from it by Jalview. The desktop application can also interact
-with `two-way' remote analysis services in order to offload computationally
-intensive tasks to High Performance Computing facilities. Most of these two-way
-services are provided by {\bf Ja}va {\bf B}ioinformatics {\bf A}nalysis {\bf
-W}eb {\bf S}ervice (JABAWS) servers\footnote{See
-http://www.compbio.dundee.ac.uk/jabaws for more information and to download
-your own server.}, which provides an easily installable system for performing
-a range of bioinformatics analysis tasks. }
-\parbox[c]{1.75in}{\includegraphics[width=1.65in]{images/wsmenu.pdf}}
-
-\subsection{One-Way Web 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.
-
-\subsection{Remote Analysis Web Services}
-Remote analysis services enable Jalview to use external computational
-facilities. There are curently three types of service - multiple sequence
-alignment, protein secondary structure prediction, and alignment analysis.
-Many of these are provided by JABA servers, which are described at the end of
-this section. In all cases, Jalview will construct a job based on the alignment
-or currently selected sequences, ask the remote server to run the job, monitor
-status of the job and, finally, retrieve the results of the job and display
-them. The Jalview user is kept informed of the progress of the job through a
-status window.
-
-Currently, web service jobs and their status windows are not stored in Jalview
-Project Files\footnote{This may be rectified in future versions.}, so it is
-important that you do not close Jalview whilst a job is running. It is also
-essential that you have a continuous network connection in order to
-successfully use web services from Jalview, since it periodically checks the
-progress of running jobs.
-
-
-\subsection{JABA Web Services for Sequence Alignment and Analysis}
-\label{jabaservices}
-JABA stands for ``JAva Bioinformatics Analysis'', which is a system developed
-by Peter Troshin and Geoff Barton at the University of Dundee for running
-computationally intensive bioinformatics analysis programs. A JABA installation
-typically provides a range of JABA web services (JABAWS) for use by other
-programs, such as Jalview.
-
-Exercises in the remainder of this section will demonstrate the simplest way of
-installing JABA on your computer, and configuring Jalview so it can access the JABA services. If you
-need any further help or more information about the services, please go to the
-\href{http://www.compbio.dundee.ac.uk/jabaws}{JABAWS home page}.
-%% \subsubsection{Aims}
-%% \begin{list}{$\bullet$}{}
-%% \item Gain experience using the different alignment services provided by
-% JABA
-%%\item Learn about the way that Jalview stores user presets for JABA services
-%%\item Learn how to install JABA services and configure Jalview to access them
-%%\end{list}
-
-\subsection{Changing the Web Services Menu Layout}
-\label{changewsmenulayout}
-If you are working with a lot of different JABA services, you may wish to change
-the way Jalview lays out the web services menu. You can do this from the Web
-Services tab of the {\sl Preferences} dialog box.
-
-\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 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.}
-\exstep{Hit {\sl Refresh Services} to update the web services menu -- once the
-progress bar has completed, open the {\sl Web Service} menu to view the changes.}
-\exstep{Select the {\sl Index by host} checkbox and refresh the services once again.
-
-{\sl Observe the way the layout of the JABAWS Alignment submenu changes.}
-}
-\exstep{Do the same with the {\sl Index by type} checkbox.}
-}
-
-Jalview provides these options for configuring the layout of the {\sl Web Service}
-menu because different Jalview users may have access to a different number of
-JABA services, and each will have their own preference regarding the layout of
-the menu.
-
-\begin{figure}[htbc]
-\begin{center}
-\includegraphics[width=3in]{images/jvjabawsconfig.pdf}
-\caption{{\bf The Jalview Web Services preferences panel.} Options are provided
-for configuring the list of JABA servers that Jalview will use, enabling and
-disabling Enfin services, and configuring the layout of the web services
-menu.}
-\label{jvjabawsconfig}
-\end{center}
-\end{figure}
-
-
-\subsubsection{Testing JABA services}
-The JABAWS configuration dialog shown in Figure \ref{jvjabawsconfig} has colour
-codes to indicate whether the Desktop can access the server, and whether all
-services advertised by the server are functional. The colour codes are: