{\Huge
-Jalview 2.10.0}
+Jalview 2.10.1}
\vspace{0.5in}
{\huge
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-7th October 2016
+15th February 2017
\end{center}
building, principal components analysis, physico-chemical property conservation
and sequence consensus analyses are built into the program. Web services enable
Jalview to access online alignment and secondary structure prediction programs,
-as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
+as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation.
+Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem.
+Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout.
+Alignment views are dynamically linked with Jmol and Chimera structure displays,
+a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order
+to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style
+ figure generation capabilities for the preparation of alignments for publication.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5.8in]{images/jvcapabilities.pdf}
\subsection{About this Tutorial }
This tutorial is written in a manual format with short exercises where
-appropriate, typically at the end of each section. This chapter concerns the
+appropriate, typically at the end of each section. This concerns the
basic operation of Jalview and should be sufficient for those who want to
launch Jalview (Section \ref{startingjv}), open an alignment (Section
\ref{loadingseqs}), perform basic editing (Section
In addition, the manual covers the additional visualization and
analysis techniques available in Jalview. This includes working
-with the embedded Jmol molecular structure viewer, building and viewing trees and PCA
-plots, and using trees for sequence conservation analysis. An overview of
+with the embedded Jmol molecular structure viewer and opening Chimera, building
+and viewing trees and PCA plots, and using trees for sequence conservation analysis. An overview of
the Jalview Desktop's webservices is given in Section \ref{jvwebservices}, and
the alignment and secondary structure prediction services are described
-in detail in Sections \ref{msaservices} and \ref{protsspredservices}. Section \ref{featannot} details the creation and visualization of sequence
-and alignment annotation. Section \ref{workingwithnuc} discusses
+in detail in Sections \ref{msaservices} and \ref{protsspredservices}
+respectively.
+Section \ref{featannot} details the creation and visualization of sequence and alignment annotation. Section \ref{workingwithnuc} discusses
specific features of use when working with nucleic acid sequences, such as translation and linking to protein
coding regions, and the display and analysis of RNA secondary structure.
Jalview site. This behaviour can be switched off in the Jalview Desktop
preferences dialog by unchecking the open file option.
This alignment will look like the one in Figure \ref{startpage} (taken
-from Jalview version 2.7).
+from Jalview version 2.10.1).
%[figure 3 ]
\begin{figure}[htbp]
where editing and navigation are performed using the keyboard. The {\bf F2 key}
is used to switch between these two modes. With a Mac as the F2 is
often assigned to screen brightness, one may often need to type {\bf function
- [Fn] key with F2} function
+ [Fn] key with F2 key}
[Fn]-F2.
\begin{figure}[htb]
Rapid movement to specific positions is accomplished as listed below:
\begin{list}{$\circ$}{}
\item {\bf Jump to Sequence {\sl n}:} Type a number {\sl n} then press [S] to
-move to sequence (row). {\sl n}
+move to sequence (row) {\sl n}.
\item {\bf Jump to Column {\sl n}:} Type a number {\sl n} then press [C] to move to column {\sl n} in the alignment.
\item {\bf Jump to Residue {\sl n}:} Type a number {\sl n} then press [P] to move to residue number {\sl n} in the current sequence.
\item {\bf Jump to column {\sl m} row {\sl n}:} Type the column number {\sl m}, a comma, the row number {\sl n} and press [RETURN].
`Paste to new window' option in the menu that appears. The other is to select
{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the
main menu, paste the sequences into the text window that will appear, and select
-{sl New Window} (Figure \ref{loadtext}). In both cases, presuming that they are
+{\sl New Window} (Figure \ref{loadtext}). In both cases, presuming that they are
in the right format, Jalview will happily read them into a new alignment window.
%[fig 8]
This selects the entire column of the alignment. Ranges of positions from the
alignment ruler can also be selected by clicking on the first position and then
holding down the [SHIFT] key whilst clicking the other end of the selection.
-Discontinuous regions can be selected by holding down [CTRL] and clicking on positions to add to the column selection. Note that each [CTRL]-Click changes the current selected sequence region to that column, but adds to the column selection. Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
+Discontinuous regions can be selected by holding down [CTRL] and clicking on
+positions to add to the column selection. Note that each [CTRL]-Click (PC) or
+[CMD]-Click (Mac) changes the current selected sequence region to that column,
+but adds to the column selection.
+Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
%[fig 13]
\begin{figure}[htbp]
also be output to a textbox using the output functions in the pop-up menu
obtained by right clicking the current selection. The textbox enables quick
manual editing of the alignment prior to importing it into a new window (using
-the [New Window] button) or saving to a file with the {\sl File $\Rightarrow$
-Save As } pulldown menu option from the text box.
+the {\sl New Window} button) or saving to a file with the {\sl File
+$\Rightarrow$ Save As } pulldown menu option from the text box.
\section{Reordering an Alignment}
Sequence reordering is simple. Highlight the sequences to be moved then press the up or down arrow keys as appropriate (Figure \ref{reorder}). If you wish to move a sequence up past several other sequences it is often quicker to select the group past which you want to move it and then move the group rather than the individual sequence.
resolution.}
}
-\newpage
-
-\section{Summary - the rest of the manual}
-
-The first few chapters have covered the basics of Jalview operation: from
-starting the program, importing, exporting, selecting, editing and colouring
-aligments, to the generation of figures for publication, presentation and web
-pages.
-
-The remaining chapters in the manual cover:
-
-\begin{list}{$\circ$}{}
-\item{Chapter \ref{featannot} covers the creation, manipulation and visualisation
-of sequence and alignment annotation, and retrieval of sequence and feature data
-from databases.}
-\item {Chapter \ref{msaservices} explores the range of multiple alignment
-programs offered via Jalview's web services, and introduces the use of
-AACon for protein multiple alignment conservation analysis.}
-\item {Chapter \ref{alignanalysis} introduces Jalview's built in tools for
-multiple sequence alignment analysis, including trees, PCA, and alignment
-conservation analysis. }
-\item {Chapter \ref{3Dstructure} demonstrates the structure visualization
-capabilities of Jalview.}
-\item {Chapter \ref{proteinprediction} introduces protein sequence based
-secondary structure and disorder prediction tools, including JPred.}
-\item {Chapter \ref{dnarna} covers the special functions and
-visualization techniques for working with RNA alignments and protein coding
-sequences.}
-\item {Chapter \ref{jvwebservices} provides instructions on the
-installation of your own Jalview web services.}
-\end{list}
+% left out for Glasgow 2016
+% \newpage
+%
+% \section{Summary - the rest of the manual}
+%
+% The first few chapters have covered the basics of Jalview operation: from
+% starting the program, importing, exporting, selecting, editing and colouring
+% aligments, to the generation of figures for publication, presentation and web
+% pages.
+%
+% The remaining chapters in the manual cover:
+%
+% \begin{list}{$\circ$}{}
+% \item{Chapter \ref{featannot} covers the creation, manipulation and visualisation
+% of sequence and alignment annotation, and retrieval of sequence and feature data
+% from databases.}
+% \item {Chapter \ref{msaservices} explores the range of multiple alignment
+% programs offered via Jalview's web services, and introduces the use of
+% AACon for protein multiple alignment conservation analysis.}
+% \item {Chapter \ref{alignanalysis} introduces Jalview's built in tools for
+% multiple sequence alignment analysis, including trees, PCA, and alignment
+% conservation analysis. }
+% \item {Chapter \ref{3Dstructure} demonstrates the structure visualization
+% capabilities of Jalview.}
+% \item {Chapter \ref{proteinprediction} introduces protein sequence based
+% secondary structure and disorder prediction tools, including JPred.}
+% \item {Chapter \ref{dnarna} covers the special functions and
+% visualization techniques for working with RNA alignments and protein coding
+% sequences.}
+% \item {Chapter \ref{jvwebservices} provides instructions on the
+% installation of your own Jalview web services.}
+% \end{list}
\chapter{Annotation and Features}
\label{featannot}
but are shown mapped on to specific residues within the alignment.
Features and annotation can be interactively created, or retrieved from external
-data sources. Webservices like JNet (see \ref{jpred} above) can be used to analyse a
-given sequence or alignment and generate annotation for it.
+data sources. Webservices like JPred (see \ref{jpred} above) can be used to
+analyse a given sequence or alignment and generate annotation for it.
\section{Conservation, Quality and Consensus Annotation}
You can export all the database cross references and annotation terms shown in
the sequence ID tooltip for a sequence by right-clicking and selecting the {\sl
-[Sequence ID] $\Rightarrow$ Sequence details \ldots} option from the popup menu.
+[Sequence ID] $\Rightarrow$ Sequence details \ldots} option from the popup
+menu.
A similar option is provided in the {\sl Selection} sub-menu allowing you to
obtain annotation for the sequences currently selected.
If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record.
\subsubsection{Rate of Feature Retrieval}
-Feature retrieval can take some time if a large number of sources is selected and if the alignment
-contains a large number of sequences.
+Feature retrieval can take some time if a large number of sources are selected
+and if the alignment contains a large number of sequences.
As features are retrieved, they are immediately added to the current alignment view.
The retrieved features are shown on the sequence and can be customised as described previously.
McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) {\sl Molecular
Systems Biology} {\bf 7} 539
\href{http://dx.doi.org/10.1038/msb.2011.75}{doi:10.1038/msb.2011.75}} Of these,
-T-COFFEE is slow but the accurate. ClustalW is historically
+T-COFFEE is slow but accurate. ClustalW is historically
the most widely used. Muscle is fast and probably best for
smaller alignments. MAFFT is probably the best for large alignments,
however Clustal Omega, released in 2011, is arguably the fastest and most
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
+menu, including font, scaling and label display options. 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
\subsection{Configuring the default structure viewer}
\label{configuring3dviewer}
-To configure which one is used when creating a new
+To configure which viewer 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,
\section{Automatic Association of PDB Structures with Sequences}
Jalview can automatically determine which structures are associated with a
-sequence in a number of ways.
-\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
-sequence with a Uniprot sequence and from there discover any associated PDB
-structures. This takes a few seconds and applies to all sequences in the
-alignment which have valid Uniprot IDs. On moving the cursor over the sequence
-ID the tool tip\footnote{Tip: The sequence ID tooltip can often become large for
-heavily cross referenced sequence IDs. Use the {\sl View $\Rightarrow$ Sequence
-ID Tooltip $\Rightarrow$ } submenu to disable the display of database cross
-references or non-positional features. } now shows the Uniprot ID and any
-associated PDB structures.
-
-\begin{figure}[htbp]
-\begin{center}
-%TODO fix formatting
-\parbox{1.5in}{
-{\centering
-\begin{center}
-\includegraphics[width=1.5in]{images/auto1.pdf}
-\end{center}}
-} \parbox{3.25in}{
-{\centering
-\begin{center}
-\includegraphics[scale=0.5]{images/auto2.pdf}
-\end{center}
-}
-} \parbox{1.5in}{
-{\centering
-\begin{center}
-\includegraphics[width=1.5in]{images/auto3.pdf}
-\end{center}
-}
-}
-
-\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence.
-After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and
-any associated PDB structures (right).}
-\label{auto}
-\end{center}
-\end{figure}
+sequence via its ID, and any associated database references. To do this, open
+the Sequence ID popup menu and select {\sl View 3D Structure}, to open the 3D
+Structure Chooser.
+%(Figure\ref{auto}).
+
+When the structure chooser is first opened, if no database identifiers are
+available, Jalview will attempt to discover identifiers for the sequence and from there discover any
+associated PDB structures. This can take a few seconds for each sequence and
+will be performed for all selected sequences. After this is done, you can see
+the added database references in a tool tip by mousing over the sequence
+ID\footnote{Tip:
+The sequence ID tooltip can often become large for heavily cross referenced sequence IDs. Use the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ }
+submenu to disable the display of database cross references or non-positional
+features. }, now shows the Uniprot ID and any associated PDB structures.
+%
+% \begin{figure}[htbp]
+% \begin{center}
+% %TODO fix formatting
+% \begin{center}
+% \includegraphics[width=3.5in]{images/pdbstructurechooser.pdf}
+% \end{center}
+%
+%
+% \caption{{\bf The PDB Structure Chooser dialog.} }
+% \label{auto}
+% \end{center}
+% \end{figure}
\subsection{Drag-and-Drop Association of PDB Files with Sequences by Filename
Match}
in the structure viewer can be saved as an EPS or PNG with the {\sl File
$\Rightarrow$ Save As $\Rightarrow$ \ldots} submenu, which also allows the raw
data to be saved as PDB format. The mapping between the structure and the
-sequence (How well and which parts of the structure relate to the sequence) can
+sequence (how well and which parts of the structure relate to the sequence) can
be viewed with the {\sl File $\Rightarrow$ View Mapping} menu option.
\subsubsection{Using the Jmol Visualization Interface }
\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. }
+\caption{{\bf Secondary Structure Prediction} Status (left) and results (right)
+windows for JPred predictions. }
\label{jpred}
\end{center}
\end{figure}
Jpred is launched in the same way as the other web services. Select {\sl Web
-Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
+Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JPred
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}).
reording and hiding autocalculated and sequence associated annotation. }
\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by
-clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction}
-from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear.
+clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$
+Secondary Structure Prediction $\Rightarrow$ JPred Secondary Structure
+Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear.
Note that the number of sequences in the results window is many more than in the original alignment as
-JNet performs a PSI-BLAST search to expand the prediction dataset. The results
-from the prediction are visible in the annotation panel. Jnet secondary
+JPred performs a PSI-BLAST search to expand the prediction dataset. The results
+from the prediction are visible in the annotation panel. JPred secondary
structure prediction annotations are examples of sequence-associated alignment annotation. }
% TODO: check how long this takes - about 2 mins once it gets on the cluster.
\exstep{
-Select a different sequence and perform a JNet prediction in the same way. There will probably be minor differences in the predictions.
+Select a different sequence and perform a JPred prediction in the same way.
+There will probably be minor differences in the predictions.
}
\exstep{
Select the sequence used in the second sequence prediction by clicking on its
by right clicking the mouse to open the context menu, and select the {\sl Add
Reference Annotation} option.
-{\bf All} the JNet predictions for the sequences will now be visible in the
+{\bf All} the JPred predictions for the sequences will now be visible in the
original alignment window.}
{\bf Homework:} Go back to the last step of exercise \ref{annotatingalignex} and
git://source.jalview.org / jalview-manual.git / blobdiff