\exercise{Saving Alignments}{
\label{save}
-\exstep{Launch Jalview or use close all windows.
-Load the ferredoxin
-alignment from {\bf PFAM (seed)} data base using the PFAM seed accession number
-{\bf PF03460} (see Exercise \ref{load}). } \exstep{
+\exstep{Launch Jalview afresh, or use {\sl Desktop $\Rightarrow$ Window
+$\Rightarrow$ Close all }.}
+\exstep{Load the ferredoxin
+alignment ({\bf PF03460}) from {\bf PFAM (seed)} (see Exercise
+\ref{load}).
+} \exstep{
Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a
location into which to save the alignment and select your preferred format. All
\label{exselect}
\exstep{Close windows.
-Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM seed} database).
+Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
}
\exstep{Selecting an arbitrary region. Choose a residue and place the mouse
cursor on it (residue information will show in alignment window status
\end{figure}
\exercise{Reordering the Alignment}{
-\exstep{Close all windows in Jalview from desktop menu. Load the ferredoxin
-alignment using the PFAM domain PF03460 from PFAM seed database.
-Select one of the sequence in the sequence ID panel, use the up and down
+\exstep{Close windows.
+
+Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
+}
+\exstep{Select one of the sequence in the sequence ID panel, use the up and down
arrow keys to alter the sequence's position in the alignment. (Note that
this will not work in cursor mode)}
\exstep{To select and move multiple
Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group.
\exercise{Hiding and Revealing Regions}{
-\exstep{Close all windows, open the PFAM accession PF03460 from the PFAM (seed)
-database.
-Select a contiguous set of sequences by clicking and dragging on the sequence ID panel.
+\exstep{Close windows.
+
+Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
+}
+\exstep{Select a contiguous set of sequences by clicking and dragging on the sequence ID panel.
Right click on the selected sequence IDs to bring up the sequence ID context
menu, select {\sl Hide Sequences}.
}
\href{http://www.jalview.org/examples/exampleFile.jar}
{http://www.jalview.org/examples/exampleFile.jar}.
-{\sl {\bf Mac Users: Please use the Apple or [CMD] key in place of [CTRL]
-for key combinations such as [CTRL]-A.} }
+{\sl {\bf Mac Users:} Please use the Apple or [CMD] key in place of [CTRL]
+for key combinations such as [CTRL]-A. }
Remember to use [CTRL]-Z to undo an edit, or the {\sl File $\Rightarrow$
Reload } function to revert the alignment back to the original version if you
{This continues on from the previous exercise, and recreates the final part of the example ferredoxin
alignment from the unaligned sequences using Jalview's keyboard editing mode.
-{\bf Note:} For Mac users, [CTRL]-[SPACE] command
-has the same effect as the [SHIFT]-[SPACE] command mentioned in this exercise.
-Window users should use [SHIFT]-[SPACE] rather than the [CTRL]-[SPACE] command,
-as this command will close the window.
+{\bf Window users:} Please {\em only use} [SHIFT]-[SPACE] in this
+exercise.
+
+{\bf Mac users:} [CTRL]-[SPACE] can also be used instead of [SHIFT]-[SPACE].
\exstep{Load the sequence alignment at
\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the
}
\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}).
+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]
row entry in the file, and create an annotation row grouping to overlay the three quantitative
annotation rows.}
}
+\exstep{{\bf Homework for after you have completed exercise \ref{secstrpredex}:}
\label{viewannotfileex}
- {\sl Homework for after you have completed exercise \ref{secstrpredex}:}
-Recover or recreate the secondary structure prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export
- Annotation} function to view the Jnet secondary structure prediction annotation row.
+Recover or recreate the secondary structure predictions that you made from
+JPred. Use the {\sl File $\Rightarrow$ Export Annotation} function to view the Jnet secondary structure prediction annotation row.
Note the
SEQUENCE\_REF statements surrounding the row specifying the sequence association for the
-annotation. }
+annotation.
+}}
\section{Importing Features from Databases}
however Clustal Omega, released in 2011, is arguably the fastest and most
accurate tool for protein multiple alignment.
+\section{Performing a multiple sequence alignment}
To run an alignment web service, select the appropriate method from the {\sl
Web Service $\Rightarrow$ Alignment $\Rightarrow$ \ldots} submenu (Figure
\ref{webservices}). For each service you may either perform an alignment with
using the `Algorithm ordering' entry within the {\sl Calculate $\Rightarrow$
Sort } sub menu.
-\subsubsection{Realignment}
+\subsection{Realignment to add sequences to an existing alignment}
The re-alignment option is currently only supported by Clustal
Omega and ClustalW. When performing a re-alignment, Jalview submits the
-current selection to the alignment service complete with any existing gaps. This
-approach is useful when one wishes to align additional sequences to an existing alignment without
-any further optimisation to the existing alignment. The re-alignment service
-provided by ClustalW in this case is effectively a simple form of profile
-alignment.
+current selection to the alignment service complete with any existing gaps.
+Realignment with ClustalW is useful when one wishes to align
+additional sequences to an existing alignment without any further optimisation
+to the existing alignment. ClustalO's realignment works by generating a
+probabilistic model (a.k.a HMM) from the original alignment, and then realigns
+{\bf all} sequences to this profile. For a well aligned MSA, this process
+will simply reconstruct the original alignment (with additonal sequences), but
+in the case of low quality MSAs, some differences may be introduced.
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsubsection{Alignments of Sequences that include Hidden Regions}
-If the view or selected region that is submitted for alignment contains hidden
+\subsection{Alignments of Sequences that include Hidden Regions}
+If the view or selected region submitted for alignment contains hidden
regions, then {\bf only the visible sequences will be submitted to the service}.
Furthermore, each contiguous segment of sequences will be aligned independently
(resulting in a number of alignment `subjobs' appearing in the status window).
columns can be used to preserve existing parts of an alignment whilst the
visible parts are locally refined.
-
-\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.
+\subsection{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.
\exercise{Multiple Sequence Alignment}{
\exstep{ Close all windows and open the alignment at {\sf
\url{http://www.jalview.org/training/Training-Videos}.}
}
+\section{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}
+\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}
+
+\subsection{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}
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,
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
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 $\Rightarrow$
+\subsection{Enabling and Disabling AACon Calculations}
+When the AACon Calculation entry in the {\sl Web Service $\Rightarrow$
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
+\subsection{Configuring which AACon Calculations are Performed}
+The {\sl Web Service $\Rightarrow$ 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
AACon settings for an alignment are saved in Jalview projects along with the
latest calculation results.
-\subsubsection{Changing the Server used for AACon Calculations}
+\subsection{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 $\Rightarrow$
+another AACon service by selecting it from the {\sl Web Service $\Rightarrow$
Conservation $\Rightarrow$ Switch Server} submenu.
\chapter{Analysis of Alignments}
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 chapter \ref{jvwebservices}.
-In this section, we describe the built-in analysis capabilities common to both
-the Jalview Desktop and the JalviewLite applet.
+Jalview {\sl via} web services - and found under the
+{\sl Web Service} menu. In this section, we describe the built-in analysis
+capabilities common to both the Jalview Desktop and the JalviewLite applet.
\section{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
+Principal components analysis calculations create 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 each sequence as a point in
3D `similarity space'. Sets of similar sequences tend to lie near each other in
this space.
\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.
+\caption{{\bf Calculating Trees} Jalview provides a range of options
+for calculating trees.
Jalview can also load precalculated trees in Newick format (right).}
\label{trees1}
\end{center}
\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
or in the Development section of the Jalview web site
(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds})
-in the table, go to ``latest official build'' row and ``Webstart'' column, click on ``G2''.)}
+in the table, go to ``latest official build'' row and ``Webstart'' column, click
+on ``2G''.)}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour
\end{figure}
-\chapter{Working with 3D structures}
-\label{3Dstructure}
-Jalview can interactively view 3D structure using Jmol or Chimera. Whether Jmol or Chimera is
-the default structure viewer of choice is set from {\sl Preferences}, go
-to {\sl Tools $\Rightarrow$ Preferences\ldots} and select either JMOL or
-CHIMERA in the {\sl Structure} tab.
-
% To review, Chapter \ref{featannot} describes the mechanisms provided by
% Jalview for interactive creation of sequence and alignment annotation, and how
% they can be displayed, imported and exported and used to reorder the alignment. Chapter
% and Section \ref{workingwithrna} covers the visualization,
% editing and analysis of RNA secondary structure.
-\section{Working with Structures}
+\chapter{Working with 3D structures}
+\label{3Dstructure}
\label{wkwithstructure}
-Jalview facilitates the use of protein structures for the analysis of alignments
-by providing a linked view of structures associated with sequences in
-the alignment. The Java based molecular viewing program Jmol\footnote{See the
-Jmol homepage \url{http://www.jmol.org} for more information.} has been
-incorporated\footnote{Earlier versions of Jalview included MCView - a simple
-main chain structure viewer. Structures are visualized as an alpha carbon trace
-and can be viewed, rotated and coloured in a structure viewer and the results
-interpreted on a sequence alignment.} which enables sophisticated molecular
-visualizations to be prepared and investigated alongside an analysis of
-associated sequences.
-PDB format files can be imported directly or structures can be retrieved from
-the European Protein Databank (PDBe) using the Sequence Fetcher (see
-\ref{fetchseq}).
-
-\subsection{Automatic Association of PDB Structures with Sequences}
+Jalview facilitates the use of 3D structure data for the analysis of alignments
+by providing a linked view of structures associated with the aligned sequences.
+It also allows sequence, secondary structure and B-factor data to be imported
+from structure files, and supports the use of the EMBL-EBI's SIFTS database to
+construct accurate mappings between UniProt protein sequences and structures
+retrieved from the PDB.
+
+\section{Molecular graphics systems supported by Jalview}
+Jalview can interactively view 3D structure using Jmol, a Java based molecular
+viewing program\footnote{See the Jmol homepage \url{http://www.jmol.org} for
+more information.} integrated with Jalview.\footnote{Earlier
+versions of Jalview included MCView - a simple main chain structure viewer.
+Structures are visualized as an alpha carbon trace and can be viewed, rotated
+and coloured in a structure viewer and the results interpreted on a sequence
+alignment.} It also supports the use of UCSF Chimera, a powerful molecular
+graphics system that needs separate installation. Jalview can also read PDB and
+mmCIF format files directly to extract sequences and secondary structure
+information, and retrieve records from the European Protein
+Databank (PDBe) using the Sequence Fetcher (see \ref{fetchseq}).
+
+\subsection{Configuring the default structure viewer}
+\label{configuring3dviewer}
+To configure which one is used when creating a new
+structure view, open the Structures preferences window {\sl via} {\sl Tools $\Rightarrow$ Preferences\ldots} and
+select either JMOL or CHIMERA as the default viewer. If you select Chimera,
+Jalview will search for the installed program, and if it cannot be found,
+you will be prompted to locate the Chimera binary, or directed to the UCSF
+Chimera download page.
+
+\section{Automatic Association of PDB Structures with Sequences}
Jalview can automatically determine which structures are associated with a
sequence in a number of ways.
-\subsubsection{Discovery of PDB IDs from Sequence Database Cross-references}
+\subsection{Discovery of PDB IDs from Sequence Database Cross-references}
If a sequence has an ID from a public database that contains cross-references to
the PDB, such as Uniprot. Right-click on any sequence ID and select {\sl Structure $\Rightarrow$
Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (Figure \ref{auto}). Jalview will attempt to associate the
\end{center}
\end{figure}
-\subsubsection{Drag-and-Drop Association of PDB Files with Sequences by Filename
+\subsection{Drag-and-Drop Association of PDB Files with Sequences by Filename
Match}
\label{multipdbfileassoc}
If one or more PDB files stored on your computer are dragged from their location
\end{figure}
-\subsection{Viewing Structures}
+\section{Viewing Structures}
\label{viewAllStructures}
The structure viewer is launched from the sequence ID context
menu. To view a particular structure associated with a sequence in the
automatic application of colour schemes when new structure data is added, or
when associated alignment views are modified.
-\exercise{Viewing Structures in Jmol viewer}{\label{viewingstructex}
-\exstep{Load the alignment at
+\exercise{Viewing Structures with the integrated Jmol
+Viewer}{\label{viewingstructex} \exstep{Load the alignment at
\textsf{http://www.jalview.org/examples/exampleFile.jar}.}
\exstep{Right-click on the
sequence ID label of {\sl FER1\_SPIOL} to open
-the context menu. Select {\sl 3D Structure}, this
-opens a Structure Chooser window, select { \sl 1A70} and click {\sl View}.
-
-{\sl Note: the Structure Chooser interface
-provides a smart technique for selecting PDB structures by queryingthe meta-data
-of structures. Extra information can be including in this window by checking boxes
-in the columns of the ``Customise Displayed Options'' tab}.
+the ID popup menu and select {\sl 3D Structure}. After a short pause, a
+Structure Chooser dialog will open for the sequence, listing available
+structure data from the PDB. Select { \sl 1A70} from the list and click {\sl
+View}.
+
+{\sl The Structure Chooser dialog presents available PDB structures
+by querying the EMBL-EBI's PDBe web API. Extra information can be
+including in this window by checking boxes in the columns of the ``Customise Displayed Options'' tab}.
% JBP Note: Bug JAL-1238 needs to be fixed ASAP
}
\exstep{By default the Jmol
correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view
happens automatically if a
structure is added to an existing Jmol display using
-{\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} to open the Structure Chooser dialog box.
-Select structures required and select {\sl View}. A new Jmol view
+the {\sl 3D Structure } option in the Sequence ID popup menu to open the
+Structure Chooser dialog box.
+Select the structures required and select {\sl View}. A new Jmol view
opens containing superposed structures if the current selection contains two or more sequences with associated
structures.
the cartoon style, with other parts of the molecule drawn in wireframe. The Jmol
console, which has been opened after the superposition was performed, shows the
RMSD report for the superposition.
-Full information about the superposition is also outputted to the Jalview
+Full information about the superposition is also reported on the Jalview
console.\footnote{The Jalview Java Console is opened from {\sl Tools
$\Rightarrow$ Java Console} option in the Desktop's menu bar} This output also
includes the precise atom pairs used to superpose structures.
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 one of the PDB file associated with
-FER1\_MAIZE (eg. 3B2F). 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 {\sl Yes} button.
-
-{\sl The Jmol view will update to show both structures, and one will be
+\ref{viewingstructex}}
+
+\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_SPIOL
+by right-clicking its ID (CMD-click on Macs), and selecting {\sl $\Rightarrow$
+3D Structure Data \ldots } }
+
+\exstep{Pick 1A70 from the Structure Chooser dialog, and click the {\bf View}
+button. 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 {\sl Yes}.
+
+{\sl The Jmol view should 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
-(The easiest way to achieve this is to select column 121-132, and in the View
-menu selected ``All but selected region'' from the Hide options).
-
-{\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.}
+Jmol submenu}.
+}
+
+\exstep{Create a new view on the alignment, and hide all but columns 121
+through to 132 (you can do this via {\sl View $\Rightarrow$ Hide $\Rightarrow$
+All but selected region}).}
+\exstep{Select the newly created view in the {\sl Jmol $\Rightarrow$ Superpose
+With } submenu, and then recompute the superposition with {\sl Jmol
+$\Rightarrow$ Align Structures}.
+
+{\sl Note how the molecules shift position when superposed with only a small
+region of the alignment.}}
+
+\exstep{Compare RMSDs obtained when superimposing molecules with
+columns 121-132 and with the whole alignment.}
+
\exstep{The RMSD report can be
-viewed by right clicking the mouse on Jmol window, and select ``Show" and
-``Measurements". Which view do you think give the best 3D
-superposition, and why ?} }
+viewed by right clicking the mouse on Jmol window, and select {\sl
+Console} from the menu (if nothing is shown, recompute the superposition after
+displaying the console).
+
+Which view do you think give the best 3D superposition, and why ?} }
\subsubsection{Colouring Complexes}
\label{complexstructurecolours}
\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
+\exstep{Launch the Jalview desktop and ensure you have at least 1G 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}.}
-{\sl Alternatively in the Development section of the Jalview web site
-(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds})
-in the ``latest official build'' row in the table, go to the
-``Webstart'' column, click on ``G2''.}}
-\exstep{Retrieve the following {\bf full} PFAM alignments: PF02008, PF01426
-(make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.} \exstep{Drag the URL or file of 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.}
+{\sl See section \ref{memorylimits} for how to do this or click the following
+link:
+
+\url{http://www.jalview.org/services/launchApp?jvm-max-heap=2G} }}
+
+\exstep{Retrieve the following PFAM alignments from the {\bf PFAM (full)} source
+:
+PF02008 PF01426 PF00145 (enter all three - they
+will each be retrieved into their own alignment window).}
+
+\exstep{Drag the URL or file of 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{Use the Find dialog to locate every DNMT1\_MOUSE sequence in the
+alignment and for each one, open the Structure Chooser via the ID popup
+menu ({\sl $\Rightarrow$ 3D Structure Data }. Select the DNMT1\_MOUSE.pdb
+structure from the `Cached Structures' view, and click {\bf View}.
+
+{\em Part of the newly opened structure will be coloured the same way as
+the associated DNMT1\_MOUSE sequence is in the alignment view.}
+
+{\bf WARNING: do not select all sequences and open the Structure Chooser
+!} {\em This will cause Jalview to attempt to discover all structures for
+sequences in the alignment.}
+}
+\exstep{Repeat the previous two steps for each of the other
+alignments. In each case, after selecting the DNMT1\_MOUSE.pdb structure and
+hitting the `View' button on the Structure Chooser dialog, Jalview will ask if you wish to create
+a new Jmol view. Respond {\bf `Yes'} each time. This will ensure ensure each sequence
+fragment is associated with the {\bf 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.
+
+{\sl The different shading schemes will allow regions of strong physicochemical conservation are
+highlighted on the domains in the structure.}
+}
+
\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}.
+Annotation\ldots } option in each alignment window to shade the alignment by the
+{\bf Conservation} annotation row (introduced 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.
+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 Examine the regions strongly coloured at the interfaces betweeen each
+protein domain, and the DNA binding region. What do you think these patterns
+mean ? } }
+\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
}
% TODO
-\chapter{Protein Prediction Analysis}
+\chapter{Protein sequence analysis and structure prediction}
\label{proteinprediction}
+
+Many of Jalview's sequence feature and annotation capabilities were developed to
+allow the results of sequence based protein structure prediction methods to be
+visualised and explored. This chapter introduces services integrated with the
+Jalview Desktop for predicting protein secondary structure and protein disorder.
+
\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
+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
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
-Service $\Rightarrow$ 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}
\end{center}
\end{figure}
-\subsubsection{Hidden Columns and JNet Predictions}
+
+Jpred is launched in the same way as the other web services. Select {\sl Web
+Service $\Rightarrow$ 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.
+
+\subsection{Hidden Columns and JNet 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
a large loop insertion, hiding that section prior to submitting the JNet
-prediction can produce different results. In some cases, these secondary structure predictions can be more reliable for sequence on either side of the insertion\footnote{This, of course, cannot be guaranteed.}. Prediction results returned from the service will
-be mapped back onto the visible parts of the sequence, to ensure a single frame
-of reference is maintained in your analysis.
+prediction can produce different results. In some cases, these secondary
+structure predictions can be more reliable for sequence on either side of the
+insertion\footnote{This, of course, cannot be guaranteed.}. Prediction results
+returned from the service will be mapped back onto the visible parts of the
+sequence, to ensure a single frame of reference is maintained in your analysis.
-\section{Protein Disorder Prediction}
-\label{protdisorderpred}
-
-Disordered regions in proteins were classically thought to correspond to
-``linkers'' between distinct protein domains, but disorder can also play a role in
-function. The {\sl Web Service $\Rightarrow$ Disorder} menu in the alignment window
-allows access to protein disorder prediction services provided by the configured
-JABAWS servers.
-
-\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.
-As a consequence, disorder predictor results include both sequence features and
-sequence associated alignment annotation rows. Section \ref{featannot} describes
-the manipulation and display of these data in detail, and Figure
-\ref{alignmentdisorder} demonstrates how sequence feature shading and
-thresholding (described in Section \ref{featureschemes}) can be used to
-highlight differences in disorder prediction across aligned sequences.
\exercise{Secondary Structure Prediction}{
\label{secstrpredex}
}
+\section{Protein Disorder Prediction}
+\label{protdisorderpred}
+
+Disordered regions in proteins were classically thought to correspond to
+``linkers'' between distinct protein domains, but disorder can also play a role in
+function. The {\sl Web Service $\Rightarrow$ Disorder} menu in the alignment window
+allows access to protein disorder prediction services provided by the configured
+JABAWS servers.
+
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5in]{images/disorderpredannot.pdf}
+\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A
+zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disordered regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
+\label{alignmentdisorderannot}
+\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.
+As a consequence, disorder predictor results include both sequence features and
+sequence associated alignment annotation rows. Section \ref{featannot} describes
+the manipulation and display of these data in detail, and Figure
+\ref{alignmentdisorder} demonstrates how sequence feature shading and
+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}
\end{center}
\end{figure}
-\subsubsection{Navigating Large Sets of Disorder Predictions}
+\subsection{Navigating Large Sets of Disorder Predictions}
Figure \ref{alignmentdisorderannot} shows a single sequence annotated with
a range of disorder predictions. Disorder prediction annotation rows are
the associated sequence in the alignment display, and double clicking will
select that sequence.
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=5in]{images/disorderpredannot.pdf}
-\caption{{\bf Annotation rows for several disorder predictions on a sequence}. A
-zoomed out view of a prediction for a single sequence. The sequence is shaded to highlight disordered regions (brown and grey), and the line plots below the Sequence show the raw scores for various disorder predictors. Horizontal lines on each graph mark the level at which disorder predictions become significant. }
-\label{alignmentdisorderannot}
-\end{center}
-\end{figure}
-
\subsection{Disorder Predictors provided by JABAWS 2.0}
For full details of each predictor and the results that Jalview can display,
\exercise{Protein Disorder Prediction}{
%\label{protdispredex}
+{\sl Before starting this exercise, make sure you enable the \protect{`Add
+Temperature Factor'} option in your {\bf Structures} preferences. }
\exstep{Open the alignment at:
-\url{http://www.jalview.org/tutorial/interleukin7.fa}. } also available at
+\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
-
-\url{http://www.jalview.org/tutorial/training-materials/2014/Dundee/Oct/interleukin7.fa}
-
-\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Services
+\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Service
$\Rightarrow$ Disorder Prediction } submenu.}
-\exstep{Use {\sl Sequence ID $\Rightarrow$ Structure $\Rightarrow$ Discover PDB
-IDs} to retrieve all the PDB structures for the sequences.}
-
-\exstep{Open and align
-the structures for all sequences. (
-
-{\sl Hint: see \ref{viewAllStructures} to see
-how to do this.})}
+\exstep{Select all the sequences, and open the Structure Chooser via the {\sl
+Sequence ID $\Rightarrow$ 3D Structure Data\ldots } popup menu. Hit the
+{\bf View} button to retrieve and show all PDB structures for the sequences.}
\exstep{Compare the disorder predictions to the structure data by mapping any
available temperature factors to the alignment {\sl via} the {\sl Sequence ID
sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog to shade
the sequences by the long and short disorder predictors.
-Do the two methods agree with the structure ?}}
+{\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{Performing RNA Secondary Structure Predictions}
Secondary structure consensus calculations can be performed by enabling the
-VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+VIENNA service {\sl via} the {\sl Web Service $\Rightarrow$ Secondary
Structure} menu. These consensus structures are created by analysing the
covariation patterns in all visible sequences on the alignment. For more
information see the VIENNA documentation.
\includegraphics[width=5in]{images/rnaViennaServiceWindow.pdf}
\caption{Secondary structure consensus calculations can be performed by enabling the
-VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
+VIENNA service {\sl via} the {\sl Web Service $\Rightarrow$ Secondary
Structure} menu.}
\end{center}
\exercise{Viewing RNA Structures}
{ \label{viewingrnaex}
-\exstep{Import RF00162 from Rfam (Full) using {\sl Fetch sequence(s)} option in
-{\sl File} menu.}
-\exstep{Select {\sl Colour by RNA Helices} to shade the alignment by
-the secondary structure annotation provided by Rfam.}
+\exstep{Import RF00162 from the Rfam (Seed) source using {\sl Fetch sequence(s)}
+from the Desktop's File menu.}
+
+\exstep{Select {\sl Colour by RNA Helices} to
+shade the alignment by the secondary structure annotation provided by Rfam.}
\exstep{Open VARNA with {\sl Structure $\Rightarrow$ View Structure
$\Rightarrow$ RNA Secondary Structure}.
In the VARNA Structures Manager toggle between (i) secondary structure
(alignment) (with gaps) and (ii) trimmed secondary structure (alignment).
Explore the difference between trimmed and untrimmed views.
-Click on different residues and located them in the sequence alignment window.}
+Click on different residues in the VARNA diagram - you should also see them
+highlighted and selected in the sequence alignment window.}
\exstep{In the VARNA Structures Manager, right click on display window to
-bring up the pop up context menu. Investigate option within File, Export, Display
-and Edit sections.}
+bring up the pop up context menu. Explore the options within the File, Export,
+Display and Edit sections.
+
+{\em VARNA views are stored in Jalview project files, in the same way as 3D
+structure views produced by Jmol and Chimera.}}
-\exstep{Perform a secondary structure prediction in {\sl Web Services}. Enable
-the VIENNA consensus calculation via the {\sl Web Services} menu and select
-Change RNAAIiFold settings option.}
+\exstep{Enable the calculation and display of an RNAAliFold secondary structure
+prediction for the alignment by selecting {\sl Web Service $\Rightarrow$ Secondary
+Structure Prediction $\Rightarrow$ RNAAliFold }.}
% Compare this with the annotationline provided by Rfam.
-\exstep{Edit the VIENNA calculation settings to show
+\exstep{Edit the RNAAliFold calculation settings to show
Base Pair probabilities. Explore how editing the alignment affects the consensus
calculation.}
-\exstep{Import 2GIS from PDB database using {\sl Fetch sequence(s)} option.}
+\exstep{Import 2GIS from the PDB database into a new window with {\sl Fetch
+sequence(s)}.}
+
\exstep{Click on a sequence in Sequence ID panel and select {\sl Structure
$\Rightarrow$ View Structure $\Rightarrow$ 2GIS}, to view the structure in Jmol
window. Click on different residues and located them in the sequence alignment window.}
+
%\exstep{Add and link a Jmol structure view
%for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
%structure along-side the consensus structure for the alignment by adding
git://source.jalview.org / jalview-manual.git / commitdiff