% how the hell do we add another panel with text like : This tutorial introduces
% the user to the features of Jalview, a multiple sequence alignment editor and
-% viewer available from http://www.jalview.org to the title page.
+% viewer available from https://www.jalview.org to the title page.
% \renewcommand{menustyle}{\tt} %do something more advanced here.
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-24th September 2020
+25th September 2020
\end{center}
\end{center}
\end{figure}
-This tutorial is based on the Jalview
-Desktop application. Much of the information will also be useful for users of
-the JalviewJS, which has the same core editing, analysis and visualization capabilities. The Jalview Desktop, however, is much more powerful, and
-includes additional support for interaction with external web services, and
-production of publication quality graphics.
-
-The Jalview Desktop can be run in two ways; as an application launched from the
-web {\sl via} Java webstart, or as an application loaded onto your hard drive.
-The webstart version is launched from the `Launch Jalview Desktop
-button' at the top right hand side of pages of the website
-\href{http://www.jalview.org}{(www.jalview.org)}.
-To download the locally installable version, follow the links on the download
-page
-\href{http://www.jalview.org/download}{(www.jalview.org/download) }
- (Figure \ref{download}).
-These links will launch the latest stable release of Jalview.\par
-
-%% this paragraph needs to be rewritten for the new signed certificate from Certum.
-
-When the application is launched with webstart, dialogs may appear before
-the application starts. If your browser is not set up to handle webstart, then
-clicking the launch link may download a file that needs to be opened
-manually, or prompt you to select the program to handle the webstart
-file. If that is the case, you will need to locate the {\bf javaws} program
-on your system\footnote{The file that is downloaded will have a type of {\bf
-application/x-java-jnlp-file} or {\bf .jnlp}. The {\bf javaws} program that can run
-this file is usually found in the {\bf bin} directory of your Java
-installation}. Once java webstart has been launched, you may also be prompted to
-accept a security certificate signed by the Barton Group.\footnote{On some
-systems, the certificate may be signed by 'UNKNOWN'. In this case, clicking
-through the dialogs to look at the detailed information about the certificate
-should reveal it to be a Barton group certificate.} You can always trust us, so
-click trust or accept as appropriate. The splash screen (Figure \ref{splash})
-gives information about the version and build date that you are running,
+This tutorial is based on the Jalview Desktop application. Much of the
+information will also be useful for users of the JalviewJS, which has the same
+core editing, analysis and visualization capabilities. The Jalview Desktop,
+however, is much more powerful, and includes additional support for interaction
+with external web services, powerful molecular graphics programs, and production
+of publication quality graphics.
+
+The Jalview Desktop application can be downloaded from the download link on the
+Jalview website, which takes you to
+\href{https://www.jalview.org/download}{(www.jalview.org/download)}. The page
+automatically displays the options available for your computer (e.g. if you have
+Mac or PC), and a button to show all available downloads. These include special
+'executable Jar' distributions useful if you want to run a specific version of
+Jalview.
+To ensure you are running the latest version of Jalview, we recommend
+downloading the Jalview Desktop Installer package for your platform, clicking on
+the downloaded file and following the instructions to install it.
+Once installed, the Jalview Application will automatically update itself when a
+new version is released.
+
+When the Jalview Desktop application is launched, you will first see a loading
+screen whilst it checks for updates, then the program will start with the
+Jalview splash screen (Figure \ref{splash}).
+This gives information about the version and build date that you are running,
information about later versions (if available), and the paper to cite in your
-publications. This information is also available on the Jalview web site at
-\url{http://www.jalview.org}.
+publications. This information is also available on the Jalview web site at
+\url{https://www.jalview.org}.
%[fig 2]
\begin{figure}[htbp]
\end{center}
\end{figure}
-
-\subsubsection{Jalview News RSS Feed}
-
-Announcements are made available to users of the
-Jalview Desktop {\sl via} the Jalview Newsreader. This window will open
-automatically when new news is available, and can also be accessed {\sl via} the
-Desktop's {\sl Tools $\Rightarrow$ Show Jalview News} menu entry.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[height=3in]{images/jvrssnews.pdf}
-\caption{{\bf The Jalview News Reader.} The newsreader opens automatically
-when new articles are available from the Jalview Desktop's news channel.}
-\label{jalviewrssnews}
-\end{center}
-\end{figure}
-
-
\exercise{Launching Jalview from the Jalview Website}{
\label{start}
\exstep{Open the Jalview web site
-\href{http://www.jalview.org}{(www.jalview.org)}
-in your web browser. Launch Jalview by clicking on the
-pink `Launch Jalview' Desktop button in the top right hand corner. This
-will download and open a jalview.jnlp webstart file.}
-\exstep {Dialog boxes
-will open and ask if you want to open the jalview.jnlp file as the file is an application downloaded from the
-Internet, click {\sl Open}. (Note you may be asked to update Java, if you agree
-then it will automatically update the Java software). As Jalview opens, four demo
-Jalview windows automatically load.}
-\exstep {If
-you are having trouble, it may help changing the browser you are using, as the browsers and
-its version may affect this process.}
+\href{https://www.jalview.org}{(www.jalview.org)}
+in your web browser. To instal Jalview, first click the 'Download' link in the top right hand corner of the Jalview homepage. This
+will open the download webpage, the options available will reflect if you have Mac or PC computer.}
+\exstep {Download the application by clicking the download link as appropriate for your computer operating system.}
+\exstep {Instal the Jalview application by going to the download folder and
+clicking on the downloaded file, and follow the instructions.}
+\exstep {If you are having any issues, it may help changing the browser.}
\exstep{To disable opening of the demonstration project during the launch, go
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. A `Preference'
dialog box opens, untick the box adjacent to the `Open file' entry in the
`Visual' preferences tab.
Click {\sl OK} to save the preferences.}
-\exstep{Launch another Jalview workbench from the web site by clicking on the
-pink Launch button.
-The example alignment should not be loaded as Jalview starts up.}
+%%\exstep{Quit Jalview and open it again to check that the
+%%The example alignment is not loaded wehn Jalview starts up.}
\exstep{To reload the original demo file select the
{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
the URL history button (a downward arrow on the right hand side of the dialog
-box) to view the files, select exampleFile\_2\_7.jar
-(\url{http://www.jalview.org/examples/exampleFile_2_7.jar})
+box) to view the files, select exampleFile\_2\_7.jvp
+(shown as \url{https://www.jalview.org/examples/exampleFile_2_7.jvp})
then click {\sl OK}.}
\begin{list}{$\circ$}{\newline
\newline {\bf
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. Then tick the `Open file' entry of `Visual'
preferences tab, type in the URL of the sequence you want to load.}
-\item {You may want to move the jalview.jnlp file from your {\bf downloads} to another folder.}
-\item {Opening Jalview via the jnlp file will also allow Jalview to be launched offline.}
\end{list}
{\bf See the video at:
-\url{http://www.jalview.org/Help/Getting-Started}.}
+\url{https://www.jalview.org/Help/Getting-Started}.}
}
+\subsubsection{Jalview News RSS Feed}
+
+Announcements are made available to users of the
+Jalview Desktop {\sl via} the Jalview Newsreader. This window will open
+automatically when new news is available, and can also be accessed {\sl via} the
+Desktop's {\sl Tools $\Rightarrow$ Show Jalview News} menu entry.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[height=3in]{images/jvrssnews.pdf}
+\caption{{\bf The Jalview News Reader.} The newsreader opens automatically
+when new articles are available from the Jalview Desktop's news channel.}
+\label{jalviewrssnews}
+\end{center}
+\end{figure}
+
\subsection{Getting Help}
\label{gettinghelp}
\subsubsection{Built in Documentation}
navigation panel on the left hand side. To search for a specific topic, click
the `search' tab and enter keywords in the box which appears.
+\subsubsection{Email Lists}
+
+The Jalview Discussion list ({\tt jalview-discuss@jalview.org}) provides a forum
+for Jalview users and developers to raise problems and exchange ideas - any
+problems, bugs, and requests for help should be raised here. The {\tt
+jalview-announce@jalview.org} list can also be subscribed to if you wish to be
+kept informed of new releases and developments.
+
+Archives and mailing list
+subscription details can be found in the Jalview web site's \href{https://www.jalview.org/community}{community section}.
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsubsection{Email Lists}
-
-The Jalview Discussion list ({\tt jalview-discuss@jalview.org}) provides a forum
-for Jalview users and developers to raise problems and exchange ideas - any
-problems, bugs, and requests for help should be raised here. The {\tt
-jalview-announce@jalview.org} list can also be subscribed to if you wish to be
-kept informed of new releases and developments.
-Archives and mailing list
-subscription details can be found in the Jalview web site's \href{http://www.jalview.org/community}{community section}.
\section{Navigation}
\end{center}
\end{figure}
+ \exercise{Navigation}{
+\label{navigationEx}
+Jalview has two navigation and editing modes: {\bf normal} mode (where editing
+and navigation are via the mouse) and the {\bf cursor} mode (where editing and
+navigation are via the keyboard).
+The {\bf F2} key is used to switch between these two modes. With a Mac, the key
+combination {\bf Fn and F2} keys are needed, as the {\bf F2} button is
+often assigned to screen brightness. Jalview always starts up in normal mode.
+
+\exstep{Load an example alignment from its URL
+(\url{https://www.jalview.org/examples/exampleFile_2_7.jar}) via the Desktop
+using {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ from URL} dialog
+box.
+(The URL should be stored in its history and clicking on the {\sl down arrow}
+on the dialog box is an easy way to access it.)}
+\exstep{Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scroll bars.}
+\exstep{Find the Overview Window, {\sl View
+$\Rightarrow$ Overview Window} and open it. Move around the
+alignment by clicking and dragging the red box in the overview window.}
+\exstep{Return to the alignment window, look at the status bar (lower left
+hand corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
+sequence and residue under the cursor.}
+\exstep{Press [F2] key, or [Fn]-[F2] on Mac, to enter Cursor mode. Use
+the direction keys to move the cursor around the alignment.}
+\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
+{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
+two different positions if gaps are inserted into the sequence. Move to sequence 5,
+column 13 by typing {\bf 1 3 , 5} [RETURN].}
+
+{\bf Note:} To view Jalview's comprehensive on-line help documentations select
+{\sl Help} in desktop window menu, clicking on {\sl Documentation} will open a
+Documentation window. Select topics from the navigation panel on the left hand
+side or use the Search tab to locate specific key words.
+
+{\sl\bf See the video at:
+\url{https://www.jalview.org/Help/Getting-Started}.}
+}
+
\subsection{Navigation in Normal Mode}
Jalview always starts up in Normal mode, where the mouse is used to interact
\parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
}}
+
\subsection{Navigation in Cursor Mode}
\label{cursormode}
\parbox[c]{5in}{Cursor mode navigation enables the user to quickly
expressions that can be used with it.
%TODO insert a figure for the Find dialog box
-\exercise{Navigation}{
-\label{navigationEx}
-Jalview has two navigation and editing modes: {\bf normal} mode (where editing
-and navigation are via the mouse) and the {\bf cursor} mode (where editing and
-navigation are via the keyboard).
-The {\bf F2} key is used to switch between these two modes. With a Mac, the key
-combination {\bf Fn and F2} keys are needed, as the {\bf F2} button is
-often assigned to screen brightness. Jalview always starts up in normal mode.
-
-\exstep{Load an example alignment from its URL
-(\url{http://www.jalview.org/examples/exampleFile_2_7.jar}) via the Desktop
-using {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ from URL} dialog
-box.
-(The URL should be stored in its history and clicking on the {\sl down arrow}
-on the dialog box is an easy way to access it.)}
-\exstep{Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scroll bars.}
-\exstep{Find the Overview Window, {\sl View
-$\Rightarrow$ Overview Window} and open it. Move around the
-alignment by clicking and dragging the red box in the overview window.}
-\exstep{Return to the alignment window, look at the status bar (lower left
-hand corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
-sequence and residue under the cursor.}
-\exstep{Press [F2] key, or [Fn]-[F2] on Mac, to enter Cursor mode. Use
-the direction keys to move the cursor around the alignment.}
-\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
-{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
-two different positions if gaps are inserted into the sequence. Move to sequence 5,
-column 13 by typing {\bf 1 3 , 5} [RETURN].}
-
-{\bf Note:} To view Jalview's comprehensive on-line help documentations select
-{\sl Help} in desktop window menu, clicking on {\sl Documentation} will open a
-Documentation window. Select topics from the navigation panel on the left hand
-side or use the Search tab to locate specific key words.
-
-{\sl\bf See the video at:
-\url{http://www.jalview.org/Help/Getting-Started}.}
-}
-
\section{Loading Sequences and Alignments}
\label{loadingseqs}
%Jalview provides many ways to load your own sequences. %For this section of the
-% tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.
+% tutorial you will need to download the file https://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.
\subsection{Drag and Drop}
In most operating systems you can drag a file icon from a file browser
window and drop it on an open Jalview application window. The file will then be opened as a new alignment window.
\end{center}
\end{figure}
+
+\exercise{Loading Sequences}{
+\label{load}
+\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
+close all windows.}
+%% TODO: omit or combine this exercise
+%% NB. Edge (MS default browser) doesn't actually allow you to 'save' the page, apparently
+\exstep{{\bf Loading sequences from URL:} Selecting {\sl File $\Rightarrow$
+Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{https://www.jalview.org/tutorial/alignment.fa} in the box.
+Click {\sl OK} to load the alignment.}
+
+%%TODO: omit or combine
+\exstep{{\bf Loading sequences from a file:} Close all windows using the
+{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
+Then type the same URL (\url{https://www.jalview.org/tutorial/alignment.fa}) into
+your web browser. Then from the browser, save the fasta file (.fa) file to your desktop using {\sl File
+$\Rightarrow$ Save Page as}.
+Open the file you have just saved on your computer in Jalview by selecting {\sl File
+$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
+Select the file and click {\sl OK} to load.}
+
+\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
+
+(i) Drag the alignment.fa file that you have just saved on your computer from its folder and
+drop it onto the Jalview desktop window, the alignment should open.
+
+(ii) Open
+\url{https://www.jalview.org/examples/estrogenReceptorProtein.fa} in a web
+browser. Test the differences
+between (a) dragging the URL directly from browser onto the Jalview
+desktop.
+(If the URL is downloaded, alternatively locate the file in your download
+directory and drag it onto the desktop.) (b) dragging the URL from
+browser onto the existing alignment.fa alignment window in the Jalview desktop.
+
+(iii) Open \url{https://www.jalview.org/examples/estrogenReceptorCdna.fa} in a web
+browser. Note that this is a cDNA file. Drag the URL from
+browser onto the estrogenReceptorProtein.fa protein alignment window in
+the Jalview desktop. A dialogue box opens asking `Would you like to open as split
+window, with cDNA and protein linked?' select `Split Window' option. A
+split window opens in the Jalview desktop.
+}
+
+\exstep{{\bf The text editor:}
+
+(i) Open the alignment.fa file that you saved previously using text editor.
+Copy the sequence text into the clipboard using [CTRL]-A and then [CTRL]-C.
+
+(ii) Move the mouse pointer onto the Jalview desktop window's background and right-click
+to open the context window. Select the {\sl Paste to New Window} menu option.
+
+(iii) In the Jalview desktop menu, select {\sl File
+$\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox}.
+Paste the clipboard into the large window using [CTRL]-V. Click {\sl New Window}
+and the alignment will be loaded.}
+
+\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
+$\Rightarrow$ Fetch Sequences...} from the Jalview desktop menu. The {\sl
+Select Database Retrieval Source} dialog will open listing all the database
+sources. Select the {\bf PFAM seed} database and click {\sl OK}.
+
+(ii) The {\sl New
+Sequence Fetcher} window will open. Enter the accession number {\bf PF03460}
+and click {\sl OK}.
+An alignment of about 174 sequences should load.}
+\exstep{These can be viewed using the Overview window accessible from {\sl View
+$\Rightarrow$ Overview Window.}}
+{\bf See the video at:
+\url{https://www.jalview.org/Help/Getting-Started}} }
+
+
\subsection{From a URL}
Jalview can read sequence alignments directly from a URL. Please note that the
files must be in a sequence alignment format - an HTML alignment or graphics
\end{center}
\end{figure}
-
-\exercise{Loading Sequences}{
-\label{load}
-\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
-close all windows.}
-%% TODO: omit or combine this exercise
-%% NB. Edge (MS default browser) doesn't actually allow you to 'save' the page, apparently
-\exstep{{\bf Loading sequences from URL:} Selecting {\sl File $\Rightarrow$
-Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{http://www.jalview.org/tutorial/alignment.fa} in the box.
-Click {\sl OK} to load the alignment.}
-
-%%TODO: omit or combine
-\exstep{{\bf Loading sequences from a file:} Close all windows using the
-{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
-Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser. Then from the brwoser, save the fasta file (.fa) file to your desktop using {\sl File
-$\Rightarrow$ Save Page as}.
-Open the file you have just saved on your computer in Jalview by selecting {\sl File
-$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
-Select the file and click {\sl OK} to load.}
-
-\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
-
-(i) Drag the alignment.fa file that you have just saved on your computer from its folder and
-drop it onto the Jalview desktop window, the alignment should open.
-
-(ii) Open
-\url{http://www.jalview.org/examples/estrogenReceptorProtein.fa} in a web
-browser. Test the differences
-between (a) dragging the URL directly from browser onto the Jalview
-desktop.
-(If the URL is downloaded, alternatively locate the file in your download
-directory and drag it onto the desktop.) (b) dragging the URL from
-browser onto the existing alignment.fa alignment window in the Jalview desktop.
-
-(iii) Open \url{http://www.jalview.org/examples/estrogenReceptorCdna.fa} in a web
-browser. Note that this is a cDNA file. Drag the URL from
-browser onto the estrogenReceptorProtein.fa protein alignment window in
-the Jalview desktop. A dialogue box opens asking `Would you like to open as split
-window, with cDNA and protein linked?' select `Split Window' option. A
-split window opens in the Jalview desktop.
-}
-
-\exstep{{\bf The text editor:}
-
-(i) Open the alignment.fa file that you saved previously using text editor.
-Copy the sequence text into the clipboard using [CTRL]-A and then [CTRL]-C.
-
-(ii) Move the mouse pointer onto the Jalview desktop window's background and right-click
-to open the context window. Select the {\sl Paste to New Window} menu option.
-
-(iii) In the Jalview desktop menu, select {\sl File
-$\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox}.
-Paste the clipboard into the large window using [CTRL]-V. Click {\sl New Window}
-and the alignment will be loaded.}
-
-\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
-$\Rightarrow$ Fetch Sequences...} from the Jalview desktop menu. The {\sl
-Select Database Retrieval Source} dialog will open listing all the database
-sources. Select the {\bf PFAM seed} database and click {\sl OK}.
-
-(ii) The {\sl New
-Sequence Fetcher} window will open. Enter the accession number {\bf PF03460}
-and click {\sl OK}.
-An alignment of about 174 sequences should load.}
-\exstep{These can be viewed using the Overview window accessible from {\sl View
-$\Rightarrow$ Overview Window.}}
-{\bf See the video at:
-\url{http://www.jalview.org/Help/Getting-Started}} }
-
-\subsection{Memory Limits}
+ \subsection{Memory Limits}
\label{memorylimits}
Jalview 2.11 and later will automatically maximise the amount of memory available,
but if you are using an earlier version or launching Jalview in a specialised way
window's background. Should you need to increase the amount of memory available
to Jalview, full instructions are given in the built in documentation (opened by
selecting {\sl Help $\Rightarrow$ Documentation}) and on the JVM memory
-parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
+parameters page (\url{https://www.jalview.org/jvmmemoryparams.html}).
+
\section{Saving Sequences and Alignments}
\label{savingalignments}
\end{center}
\end{figure}
-\subsection{Jalview Projects}
-\parbox[c]{4in}{If you wish to save a complete Jalview session rather than
-just a single alignment (e.g. because you have calculated trees or multiple
-different alignments) then save your work as a Jalview Project
-file (.jvp).\footnote{Tip: Ensure that you have allocated plenty of memory to
-Jalview when working with large alignments in Jalview projects. See Section
-\ref{memorylimits} for how to do this.}
-From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save
-dialog box will appear. Loading a project will restore Jalview to exactly the
-view at which the file was saved, complete with all alignments, trees,
-annotation and displayed structures rendered appropriately.
-} \parbox[c]{2.3in}{ \centerline {
-\includegraphics[width=2.2in]{images/saveproj.pdf} }}
-
\exercise{Saving Alignments}{
\label{save}
\exstep{Launch Jalview afresh, or use {\sl Desktop $\Rightarrow$ Window
\exstep{Close all windows and then load the project {\sl via} the {\sl File
$\Rightarrow$ Load Project} menu option. Observe how many of the windows
reopen. Are they the same as when they were saved ? } {\bf See the video at:
-\url{http://www.jalview.org/Help/Getting-Started}.} }
+\url{https://www.jalview.org/Help/Getting-Started}.} }
+
+%% Suzanne: Jim's comment: this now appears at the end of the section, over the page from the exercise. I doubt anyone will read it there.
+\subsection{Jalview Projects}
+\parbox[c]{4in}{If you wish to save a complete Jalview session rather than
+just a single alignment (e.g. because you have calculated trees or multiple
+different alignments) then save your work as a Jalview Project
+file (.jvp).\footnote{Tip: Ensure that that plenty of memory is available to
+Jalview when working with large alignments in Jalview projects. See Section
+\ref{memorylimits} for how to check this.}
+From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save
+dialog box will appear. Loading a project will restore Jalview to exactly the
+view at which the file was saved, complete with all alignments, trees,
+annotation and displayed structures rendered appropriately.
+} \parbox[c]{2.3in}{ \centerline {
+\includegraphics[width=2.2in]{images/saveproj.pdf} }}
\chapter{Selecting and Editing Sequences }
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
} menu and select {\sl Percentage Identity}.
This will turn the selected region into a group and colour it accordingly.}
-\exstep{Hold down [CTRL] ([CMD] on Mac) or [SHIFT] and use the mouse to select and deselect sequences in
+\exstep{Hold down [CTRL] ([CMD] on Mac) and use the mouse to select and deselect sequences in
the alignment by clicking on their Sequence ID label. Note how the group expands
to include newly selected sequences, and the Percentage Identity colouring changes. }
-\exstep{ Another way to resize the group is by using the mouse to click and drag
+\exstep{ Another way to resize the group is simply to use the mouse to click and drag
the right-hand edge of the selected group.}
\exstep{The current selection can be exported and saved, place mouse on the text
\exstep{In the Alignment output window that opens, try manually editing the
alignment before clicking the {\sl New Window} button. This opens the
edited alignment in a new alignment window.} {\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
% more? change colouring style. set border colour.
}
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
+\exstep{Select one of the sequences 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
sequences, use hold [SHIFT], and select two sequences separated by
one or more un-selected sequences, repeat using the [CTRL] key. Note how
multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.}
-{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{https://www.jalview.org/training/Training-Videos}.}
}
}
\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
-\exstep{Select a region of the alignment, and experiment with the {\sl Hide all
-but selected region} option. In the alignment window menu, {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
-but selected region.}} \exstep{Select some sequences, pick one to represent the rest by hovering
+\exstep{Select a region of the alignment, and experiment with {\sl View $\Rightarrow$ Hide $\Rightarrow$ Hide all
+but selected region} and {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
+but selected region} options in the alignment window menu.} \exstep{Select some sequences, pick one to represent the rest by hovering
the mouse over this sequence. Bring up the Sequence ID context menu by right
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
with (Sequence ID name )}. To reveal these hidden sequences, right click on the
Sequence ID and in the context menu select {\sl Reveal All}.}
-{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{https://www.jalview.org/training/Training-Videos}.}
}
columns in all sequences in the selected group, and those columns are to the
right of the selected residue.
+{\bf That's it for this chapter. Don't forget the exercises on the next page!}
+\newpage
-\exercise{Editing Alignments Homework Exercise}
+\exercise{Editing Alignments}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
{
\label{editingalignex}
You are going to manually reconstruct part of the example Jalview
alignment available at
- \href{http://www.jalview.org/examples/exampleFile.jvp}
- {http://www.jalview.org/examples/exampleFile.jvp}.
+ \href{https://www.jalview.org/examples/exampleFile.jvp}
+ {https://www.jalview.org/examples/exampleFile.jvp}.
+
+ {\sl {\bf Note: this is a homework exercise for jalview course participants!}}
{\sl {\bf Mac Users:} Please use the Apple or [CMD] key in place of [CTRL]
for key combinations such as [CTRL]-A. }
want to start again.
\exstep{ Load the URL
-\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
+\textsf{https://www.jalview.org/tutorial/unaligned.fa} which contains part of the
ferredoxin alignment from PF03460.}
\exstep{ Select the first 7 sequences, and press H key to hide them (or right click
}
-\exercise{Keyboard Edits Homework Exercise}
+\exercise{Keyboard Edits}
{
\label{keyboardsex}
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: This is a homework exercise for jalview course participants}
+
{\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
+\textsf{https://www.jalview.org/tutorial/unaligned.fa}, or continue using the
edited alignment. If you continue from the
previous exercise, first right click on the sequence ID panel and select
{\sl Reveal All}. Enter cursor mode by pressing [F2] (or [Fn]-[F2] (Mac)).}
displayed, and you may have to disable it using the {\sl View $\Rightarrow$
Show Sequence Features} option before you can see your colourscheme.
-There are two main types of colouring styles: {\bf simple static residue}
+There are two main types of colouring styles: simple {\bf static residue}
colourschemes and {\bf dynamic schemes} which use conservation and consensus
analysis to control colouring. {\bf Hybrid colouring} is also possible, where
static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme}.
\exercise{Colouring Alignments}{
\label{color}
Note: Ensure that the {\sl Apply Colour
-To All Groups} flag is not selected (ie unticked) in {\sl Colour} menu in the alignment window.
+To All Groups} flag is not selected (i.e. not ticked) in {\sl Colour} menu in the alignment window.
% patch needed for 2.10 This must be turned {\sl off} specifically as it is on
% by default.
Clustalx} and note the colour change. Now try all the other colour schemes in the {\sl Colour} menu.
Note that some colour schemes do not colour all residues.}
\exstep{Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62 score}. Select a group
-of around 4 similar sequences. Use the context menu (right click on the residues in the group)
+of around 4 similar sequences. Use the context menu (opened by right clicking on the residues in the group)
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62 score} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
Slide the selector in the Conservation Colour Increment dialog box from side
to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
-Note: Feature colours overlay residue colouring and this may mask residue colouring. If this is an issue, he features colours can be
-toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}.
-{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
+Note: If you don't see any changes in appearance, it might be because sequence
+features are currently displayed (these are introduced later, in Section
+\ref{featannot}). To see if features are obscuring your colour scheme settings, look to see if the {\sl View
+$\Rightarrow$ Show Sequence Features} option in the alignment window menu is
+ticked. If it is, select it to disable feature colouring.
+
+{\bf See the video at: \url{https://www.jalview.org/training/Training-Videos}.}
}
\exstep{The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}} }
+\url{https://www.jalview.org/training/Training-Videos}.}} }
\exercise{Alignment Layout}{
\label{exscreen}
-\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jvp}.
+\exstep{Start Jalview and open the URL \textsf{https://www.jalview.org/examples/exampleFile.jvp}.
Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu.
Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
sequence ID format and so on. }
a up/down arrow symbol should appear - click on the icon, the height of the {\sl Annotation Area} can be changed
by clicking and dragging this icon up or down.}
\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
\section{Formatting and Graphics Output}
\label{layoutandoutput}
\subsubsection{Alignment and Group Colouring and Appearance}
The display of hidden row/column markers and gap characters can be turned off with {\sl Format $\Rightarrow$ Show Hidden Markers} and
-{\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area behind each residue that is coloured by the applied coloursheme.
+{\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence
+text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area
+behind each residue that is coloured by the applied colourscheme.
\subsubsection{Highlighting Nonconserved Symbols}
The alignment layout and group sub-menu both contain an option to hide
\exstep{Experiment with Jalview's other output options: try exporting an alignment view as 'BioJS', which employs the BioJS Multiple Sequence Alignment viewer. When would you use this type of export option ?}
\exstep{Working with embedded BioJSON data. Drag and drop (or load via the file browser) the 'BioJS' HTML file in the previous step. Compare the original and imported alignment views - are there differences ?}
\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.
+\url{https://www.jalview.org/training/Training-Videos}.
}
% left out for Glasgow 2016
\exercise{Annotating Alignments}{
\label{annotatingalignex}
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
+\exstep{Load the alignment at \textsf{https://www.jalview.org/tutorial/alignment.fa}.
Right-click on the label name of the {\sl Conservation} annotation row to
bring up the context menu and select {\sl Add New Row}. A dialog box will
appear asking for {\sl Annotation Name} and {\sl Annotation Description}.
annotation.
}
\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
\section{Sequence Features}
dialog box. Then, adjust the slider or enter a value in the text box to set the
threshold for displaying this type of feature.
-When a filters and complex colourschemes are applied, the configuration column will show coloured blocks or text to indicate the colouring
+When filters and complex colourschemes are applied, the configuration column will show coloured blocks or text to indicate the colouring
style and any attribute filters.
\exercise{Creating Features}{
\label{featuresex}
-\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
+\exstep{Open the alignment at \textsf{https://www.jalview.org/tutorial/alignment.fa}.
We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in
iron binding so we will create them as features. Navigate to column 97, sequence 1.
Select the entire column by clicking in the ruler bar. Then right-click on the selection
\exstep{Roll
the mouse cursor over the new features.
Note that the position given in the tool tip is the residue number, not the column number.
-To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC]. Select the [SHIFT] key,
- then insert a gap in sequence 3 at column 95 by moving the mouse.
+To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC]. Hold down the [SHIFT] key,
+ then insert a gap in sequence 3 at column 95 by moving the mouse to that position, then clicking and dragging to the right.
Roll the mouse cursor over the features and you will see that the feature has moved
with the sequence. Delete the gap you created using {\sl Edit
$\Rightarrow$ Undo}.
displayed.}
\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
\chapter{Multiple Sequence Alignment}
\label{msaservices}
\exercise{Multiple Sequence Alignment}{
\label{msaex}
\exstep{ Close all windows. Open the alignment at {\sf
-http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
+https://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}.
A window will open giving the job status. After a short time, a second window will open
with the results of the alignment.}
\exstep{Select the last three sequences in the MAFFT alignment (you may need the scroll down the alignment), and de-align them
with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect these
sequences. Then submit this view for re-alignment with {\sl ClustalO}.}
-\exstep{Return to the MAFFT alignment window in section (c), use [CTRL]-Z (undo) to
+\exstep{Return to the MAFFT alignment window in step (c), use [CTRL]-Z (undo) to
recover the alignment of the last three sequences in this MAFFT alignment.
Once the ClustalO re-alignment has completed, compare the results of
re-alignment of the three sequences with their alignment in the original MAFFT result.}
service again and explore the effect of local alignment on the non-homologous parts of the
N-terminal region.}
{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
}
\section{Customising the Parameters used for Alignment}
% alignments (refer to section \ref{superposestructs} for instructions). Which
% alignment gives the best RMSD ? }
% \exstep{Apply the same alignment parameter settings to the example alignment
-% (available from \textsf{http://www.jalview.org/examples/uniref50.fa}).
+% (available from \textsf{https://www.jalview.org/examples/uniref50.fa}).
%
% Are there differences ? If not, why not ?
% }
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.\footnote{See \url{http://www.jalview.org/help/html/calculations/pca.html}.}
+PMID: 7749921} and implemented at the SeqSpace server at the EBI.\footnote{See \url{https://www.jalview.org/help/html/calculations/pca.html}.}
%
% Jalview provides two different options for the PCA calculation: SeqSpace and
% Jalview mode. In SeqSpace mode, PCAs are computed using the identity matrix, and
\exercise{Principal Component Analysis}
{\label{pcaex}
\exstep{Load the alignment at
-\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
+\textsf{https://www.jalview.org/tutorial/alignment.fa}.}
\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
window and a dialogue box will open. Select the Principal Component Analysis option
and then click the Calculate button.}
Note how the colour of the sequence ID label matches both the colour of
the partitioned tree and the points in the PCA plot.}
{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
}
\begin{figure}[hbtp]
{\label{treeex}
\exstep{Open the alignment at
-\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
+\textsf{https://www.jalview.org/tutorial/alignment.fa}.}
\exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
window menu and a dialogue box opens. In the tree section select Neighbour
alignment for the calculation of trees.
{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
}
%\exercise{Pad Gaps in an Alignment}{
%\exstep{Open the alignment at
-% \textsf{http://www.jalview.org/tutorial/alignment.fa}. In alignment window, ensure that the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the
+% \textsf{https://www.jalview.org/tutorial/alignment.fa}. In alignment window, ensure that the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the
%alignment.}
%\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
%Neighbour Joining Using BLOSUM62}.
%{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
%{\bf See the video at:
-%\url{http://www.jalview.org/training/Training-Videos}.}
+%\url{https://www.jalview.org/training/Training-Videos}.}
%}
\exercise{Tree Based Conservation Analysis}{
it is used in the next set of exercises. }
{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
}
tree based conservation analysis exercise (exercise \ref{consanalyexerc}).}
\exstep{In the {\sl View} menu in the alignment window, select {\sl New View} to
create a new view. Ensure the annotation panel is displayed ({\sl Annotations $\Rightarrow$ Show Annotations} is toggled on). Enable the
-display of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
-Autocalculated Annotation $\Rightarrow$
-Group Consensus} submenu.}
+display of consensus annotation rows for each group by selecting the {\sl Group Consensus} option in the {\sl Annotation $\Rightarrow$
+Autocalculated Annotation } submenu.}
\exstep{Displaying the sequence
logos will make it easier to see the different residue populations within each
and dragging it up to the top of the annotations.}
\exstep{In the column alignment ruler, select a column exhibiting with about 50\%
of its residues conserved ({\em ie. about 50\% in the consensus histogram})
- that lies within the central conserved region of the alignment.}
+ that lies within the central conserved region of the alignment.
+ (Column 74 is used in \href{https://youtu.be/m-PjynicXRg}{the Tree video}).}
\exstep{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
\exstep{Switch back to the original view, and experiment with subdividing
the tree groups made in the previous exercise.}
{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
}
\begin{figure}[]
\exercise{Viewing Structures with the integrated Jmol Viewer}{
\label{viewingstructex}
\exstep{Load the alignment at
-\textsf{http://www.jalview.org/examples/exampleFile.jvp}.}
+\textsf{https://www.jalview.org/examples/exampleFile.jvp}.}
\exstep{Right-click on the
sequence ID label of {\sl FER1\_SPIOL} to open
the ID popup menu and select {\sl 3D Structure Data}. After a short pause, a
function to save the alignment as a Jalview Project (jvp). Now close the alignment and the structure view, and load the project file you just saved.
Verify that the Jmol display is as it was when you just saved the file.}
{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
}
\exercise{Aligning Structures using the Ferredoxin Sequence Alignment}{
the Chimera structure viewer sits outside the Jalview desktop and a Chimera
view window sits inside the Jalview desktop.
-{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}}
+{\bf See the video at: \url{https://www.jalview.org/training/Training-Videos}.}}
\subsection{Superimposing Structures}
Interfaces}{\label{dnmtcomplexex}
\exstep{Download the PDB file at
-\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop.
+\textsf{\url{https://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.}
The Annotations dropdown menu on the alignment window also provides options for
reordering 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
+\exstep{ Open the alignment at \url{https://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 $\Rightarrow$ JPred Secondary Structure
Prediction} from the alignment window menu. A status window will appear and after some time (about 2-4 min)
follow the instructions to view the Jalview annotations file created from the annotations
generated by the JPred server for your sequence.
\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
\begin{figure}[htbp]
\begin{center}
\subsection{Disorder Predictors provided by JABAWS 2.0}
For full details of each predictor and the results that Jalview can display,
please consult
-\href{http://www.jalview.org/help/html/webServices/proteinDisorder.html}{Jalview's
+\href{https://www.jalview.org/help/html/webServices/proteinDisorder.html}{Jalview's
protein disorder service documentation}. Short descriptions of the methods provided in JABAWS 2.0 are given below:
\subsubsection{DisEMBL}
({\sl Tool $\Rightarrow$ Preferences $\Rightarrow$ Structure)}.
\exstep{Open the alignment from
-\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
+\url{https://www.jalview.org/tutorial/interleukin7.fa}. }
\exstep{Run the DisEMBL disorder predictor {\sl via} the {\sl Web Service
$\Rightarrow$ Disorder Prediction $\Rightarrow$ Disembl with defaults}.}
Note} how well the disordered regions predicted by each method agree
with the structure.}
\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
+\url{https://www.jalview.org/training/Training-Videos}.}
\chapter{DNA and RNA Sequences}
\label{dnarna}
\exstep{Hit OK to save your preferences -- you have now added a new JABA
service to Jalview!}
\exstep{Try out your new JABA services by loading the ferredoxin sequences from
-http://www.jalview.org/tutorial/alignment.fa}
+https://www.jalview.org/tutorial/alignment.fa}
\exstep{Launch an alignment using one
of the JABA methods provided by your server. It will be listed under the JABAWS Alignment submenu of the {\sl Web Service} menu on the alignment window.
git://source.jalview.org / jalview-manual.git / blobdiff