% 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.
The Jalview Desktop application can be downloaded from the download link on the
Jalview website, which takes you to
-\href{http://www.jalview.org/download}{(www.jalview.org/download)}. The page
+\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
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}.
+\url{https://www.jalview.org}.
%[fig 2]
\begin{figure}[htbp]
\exercise{Launching Jalview from the Jalview Website}{
\label{start}
\exstep{Open the Jalview web site
-\href{http://www.jalview.org}{(www.jalview.org)}
+\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.}
\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}
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}.
+subscription details can be found in the Jalview web site's \href{https://www.jalview.org/community}{community section}.
\begin{figure}[htbp]
\begin{center}
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
+(\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}
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}.}
+\url{https://www.jalview.org/Help/Getting-Started}.}
}
\subsection{Navigation in Normal Mode}
\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.
%% 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.
+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{http://www.jalview.org/tutorial/alignment.fa}) into
+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
drop it onto the Jalview desktop window, the alignment should open.
(ii) Open
-\url{http://www.jalview.org/examples/estrogenReceptorProtein.fa} in a web
+\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.
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
+(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
\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}} }
+\url{https://www.jalview.org/Help/Getting-Started}} }
\subsection{From a URL}
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}
\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}
\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.
}
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}.}
}
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}.}
}
\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!}}
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
{\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)).}
$\Rightarrow$ 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{http://www.jalview.org/training/Training-Videos}.}
+{\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}
\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}
\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
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.}
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}.}
}
\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 / commitdiff