\vspace{2in}
-Manual Version 1.6
+Manual Version 1.7
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-1st September 2016
+12th September 2015
\end{center}
\exercise{Launching Jalview from the Jalview Website}{
\label{start}
-\exstep{Open the Jalview web
-site \href{http://www.jalview.org}{(www.jalview.org)}
+\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 {Dialogue 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 Open. (Note you maybe asked to update Java, if you agree then it
-will automatically update the Java software). As Jalview opens, four demo
+Internet, click 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
-it's version may affect this process.}
+its version may affect this process.}
\exstep{To deactivate the opening of the 4 demo sequences during the launch, go
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. A `Preference'
dialogue box opens, untick the box adjacent to the `Open file' entry in the
`Visual' preferences tab.
-Click OK to save the preferences.}
+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{To reload the original demo file select the
{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
-the URL history button on the right hand side of the dialog box to view the
-files, select exampleFile\_2\_7.jar, then click OK.}
-{\bf Note:} Should you want to reload the example alignment or load your own
+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, then click {\sl OK}.}
+{\bf Note:} Should you want to load your own
sequence during the launch process, then go
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. The tick the `Open file' entry of `Visual'
-preferences tab, type in the URL of the sequence you want to load. This
-file will load during the start up process.
+preferences tab, type in the URL of the sequence you want to load.
As the jalview.jnlp file launches Jalview on your desktop, you
may want to move this from the downloads folder to another folder.
-Opening from this file will allow Jalview to be launched offline.
+Opening from the jnlp file will allow Jalview to be launched offline.
-{\bf Help launching Jalview is available in videos on the Getting Started page
-of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}}
+{\bf A video about this exercise is available on the Jalview website at
+\url{http://www.jalview.org/Help/Getting-Started}.}
+ }
\subsection{Getting Help}
\label{gettinghelp}
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 often
-need to type function {\bf Fn key and F2}, as button is often assigned to
-screen brightness. Jalview always starts up in {\bf normal mode}.
+The {\bf F2 key} is used to switch between these two modes. With a Mac, the key
+combination {\bf Fn key and F2} is needed, as 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} is
-an easy way to access it.)}
+(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 Views
$\Rightarrow$ Overview Window} and open it. Move around the
\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 {\bf Cursor mode}. Use
+\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
column 13 by typing {\bf 1 3 , 5 [RETURN]}.}
{\bf Note:} To view Jalview's comprehensive on-line help documentations select
-Help on desktop menu, clicking on Documentation will open a Documentation
-window. Select topic from the navigation panel on the left hand side or use the
+{\sl Help} on desktop menu, clicking on {\sl Documentation} will open a
+Documentation window. Select topic from the navigation panel on the left hand side or use the
Search tab to select specific key words.
-{\bf Help navigating is available in videos on the Getting Started page
-of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}}
+
+{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
}
\section{Loading Sequences and Alignments}
\exstep{{\bf Loading sequences from URL:} Selecting File {\sl $\Rightarrow$
Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box.
-Click OK to load the alignment.}
+Click {\sl OK} to load the alignment.}
\exstep{{\bf Loading sequences from a file:} Close all windows using the
{\sl Window $\Rightarrow$ Close All} menu option from the Desktop.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser and {\bf save} the file to your desktop.
+your web browser and save the file to your desktop.
Open the file you have just saved in Jalview by selecting {\sl File
$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu and
selecting this file.
-Click OK to load.}
+Click {\sl OK} to load.}
\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
(i) Select {\sl Desktop $\Rightarrow$ Window
another window called Select Database Retrieval Source showing all the database
sources.
-Select the {\bf PFAM seed} database and click OK, then enter the accession
-number {\bf PF03460} and click OK. An alignment of about 174 sequences should
+Select the {\bf PFAM seed} database and click {\sl OK}, then enter the accession
+number {\bf PF03460} and click {\sl OK}. An alignment of about 174 sequences should
load. These can be viewed using the Overview window accessible from {\sl View
$\Rightarrow$ Overview Window.}
Several database IDs can be loaded by using semicolons to separate them.}
-{\bf Help loading sequences is available in videos on the Getting Started page
-of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
+{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
}
\section{Saving Sequences and Alignments}
\exercise{Saving Alignments}{
\label{save}
-\exstep{Launch Jalview, or use close all windows.
+\exstep{Launch Jalview or use close all windows.
Load the ferredoxin
-alignment from PFAM (seed) data base using the PFAM seed accession number
-PF03460 (see Exercise \ref{load}). } \exstep{
+alignment from {\bf PFAM (seed)} data base using the PFAM seed accession number
+{\bf PF03460} (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
and scroll red box to any part of the alignment.
Select {\sl File
$\Rightarrow$ Save Project} from the main menu and save the project in a
-suitable folder.
+suitable folder.}
-Close all windows and then load the project {\sl via} the {\sl File
+\exstep{Close all windows and then load the project {\sl via} the {\sl File
$\Rightarrow$ Load Project} menu option. Observe how all the windows and
positions are exactly as they were when they were saved. }
-{\bf Help saving sequences is available in videos on the Getting Started page
-of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}}
+{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
+}
\chapter{Selecting and Editing Sequences }
\exercise{Making Selections and Groups}{
\label{exselect}
\exstep{Close windows.
-Load the ferredoxin alignment (PF03460 from PFAM seed database).
+Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM seed} database).
Choose a residue and place the mouse
-cursor on it (Residue information will show in alignment window status
-bar)
+cursor on it (residue information will show in alignment window status
+bar).
Click and drag the mouse to create a selection. As you drag, a red box
will `rubber band' out to
show the extent of the selection.
Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
to complete the selection. Note to clear the selection press the {\bf[ESC]}
key.}
-\exstep{To create a {\bf group} from the selected the region, click the
+\exstep{To create a group from the selected the region, click the
right mouse button when mouse is on the selection, this opens a
pop-up menu in the alignment window.
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
-} menu and select `Percentage Identity'.
+} menu and select {\sl Percentage Identity}.
This will turn the selected region into a group and colour it accordingly.}
\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences in
the alignment by clicking on their Sequence ID label. Note how the group expands
\exstep{ Another way to resize the group is by using the mouse to click and drag
the right-hand edge of the selected group.}
-\exstep{The current selection can be {\bf exported} and saved by right clicking
+\exstep{The current selection can be exported and saved by right clicking
on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an
output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
\ldots} submenu.
}
-\exstep{In the alignment output window, try manually editing the alignment,
-importing group into a new alignment window by clicking the [New Window] button to import the
-file into a new alignment window.}
-{\bf Additional help is available from videos on the Jalview website at \url{http://www.jalview.org/training/Training-Videos}.}
+\exstep{Try manually editing the alignment}
+\exstep{Import the group into a new alignment window by clicking the {\sl New
+Window} button to import the file into a new alignment window.}
+{\bf A video about this exercise is available on the Jalview website
+at \url{http://www.jalview.org/training/Training-Videos}.}
% more? change colouring style. set border colour.
}
\end{figure}
\exercise{Reordering the Alignment}{
-\exstep{Close all windows in Jalview from desktop. Load the ferredoxin alignment (e.g.the
-PFAM domain PF03460 from PFAM seed).
+\exstep{Close all windows in Jalview from desktop menu. Load the ferredoxin
+alignment (e.g. the PFAM domain PF03460 from PFAM seed).
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
-sequences, use hold [SHIFT] and [CTRL], and select two sequences separated by
-one or more un-selected sequences. Note how multiple sequences are grouped
-together when they are re-ordered using the up and down arrow keys.}
-{\bf Additional help is available from videos on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}}
+sequences, use hold [SHIFT], and select two sequences separated by
+one or more un-selected sequences repeat using [CTRL]. Note how multiple
+sequences are grouped together when they are re-ordered using the up and down arrow keys.}
+{\bf A video about this exercise is available on the Jalview website
+at \url{http://www.jalview.org/training/Training-Videos}.}
+}
\section{Hiding Regions}
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. 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 pop-up
+\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.
+Right click on the selected sequence IDs to bring up the sequence ID context
menu, select {\sl Hide Sequences}.
}
\exstep{
}
\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
-\exstep{Select a region of the alignment, then add in some additional columns to
-the selection, and experiment with the `Hide all but selected region' function
-in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
-\exstep{Select some sequences and pick one to represent the rest by hovering
-the mouse over this sequence. Bring up the Sequence ID pop-up menu by right
-clicking and then select {\sl (Sequence ID name) $\Rightarrow$ Represent group
+\exstep{Select a region of the alignment, and experiment with the `Hide all but
+selected region' function in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
+\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 pop-up menu select Reveal All.}
-{\bf Additional help is available from videos on the Jalview
-website at \url{http://www.jalview.org/training/Training-Videos}}}
+Sequence ID and in the context menu select {\sl Reveal All}.}
+{\bf A video about this exercise is available on the Jalview website
+at \url{http://www.jalview.org/training/Training-Videos}.}
+}
\begin{figure}[htb]
alignment available at
\href{http://www.jalview.org/examples/exampleFile.jar}
{http://www.jalview.org/examples/exampleFile.jar}.
-Remember to use [CTRL]+Z to undo an edit, or the {\sl File $\Rightarrow$
+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
want to start again.
-If you are using OSX, and a key combination - such as [CTRL]+A - does
- not work, then try pressing the [CMD] key instead of [CTRL].
+
+{\sl Note: If you are using OSX, and a key combination - such as [CTRL]-A - does
+ not work, then try pressing the [CMD] key instead of [CTRL].}
\exstep{ Load the URL
\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
Sequences}).}
\exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
-the right so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
+the right so the initial residue A lies at column 57 using the $\Rightarrow$
+key.}
\exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
O80429\_MAIZE
two columns to the right.}
\exstep{ Now complete the
-alignment of FER1\_SPIOL with a {\bf locked edit} by pressing [ESC] and select
+alignment of FER1\_SPIOL with a locked edit by pressing [ESC] and select
columns 47 to 57 of the FER1\_SPIOL row. Move the mouse onto the G at column 50,
hold [SHIFT] and drag the G in column 47 of FER1\_SPIOL to the left by one
column to insert a gap at column 57.}
column 44, and insert 4 gaps at column 47 (after AAPM).}
\exstep{ Hold [SHIFT] and drag the I at column 39 of FER1\_MAIZE 2 columns to the
-right. Remove the gap at FER1\_MAIZE column 49 by [SHIFT]+click and drag left by
+right. Remove the gap at FER1\_MAIZE column 49 by [SHIFT]-click and drag left by
one column. Press [ESC] to clear the selection, and then insert three gaps in
FER1\_MAIZE at column 47 by holding [SHIFT] and click and drag the S in FER1\_MAIZE to the right by three columns. Finally,
remove the gap in O80429\_MAIZE at column 56 using [SHIFT]-drag to the left on
\exstep{ Use the
{\sl Edit $\Rightarrow$ Undo Edit} and {\sl Edit $\Rightarrow$ Redo Edit} menu
-option, or their keyboard shortcuts ([CTRL]+Z and [CTRL]+Y) to step
+option, or their keyboard shortcuts ([CTRL]-Z and [CTRL]-Y) to step
backwards and replay the edits you have made.}
}
columns in all sequences in the selected group, and those columns are to the
right of the selected residue.
-\section{Undoing Edits}
-Jalview supports the undoing of edits {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
-alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
-with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
-{\sl Undo} function only works for edits to the alignment or sequence ordering.
-Colouring of the alignment, showing and hiding of sequences or modification of
-annotation cannot be undone.
-
\exercise{Keyboard Edits}
-{This continues on from exercise
-\ref{mousealedit}, and recreates the final part of the example ferredoxin
+{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
\exstep{Load the sequence alignment at
\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the
-edited alignment from exercise \ref{mousealedit}. If you continue from 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].}
% TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783
insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are
now aligned.}
}
+\section{Undoing Edits}
+Jalview supports the undoing of edits {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
+alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
+with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
+{\sl Undo} function only works for edits to the alignment or sequence ordering.
+Colouring of the alignment, showing and hiding of sequences or modification of
+annotation cannot be undone.
\chapter{Colouring Sequences and Figure Generation}
\label{colouringfigures}
} \parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_rnahelix.pdf} }
-\exercise{Colouring Alignments}{
-\exstep{Ensuring that the {\sl Apply Colour To All Groups} flag is not selected
-in View sequence alignment menu.
- This must be turned {\sl off} specifically as it is {\sl on} by default.}
-\exstep{
-Open a sequence alignment, for example the PFAM domain PF03460 in PFAM seed.
-Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. 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}. Select a group
+\exercise{Colouring Alignments}{
+\label{color}
+\exstep{Ensuring that the {\sl Apply Colour To All Groups} flag is not selected in {\sl View} menu in the alignment window.
+This must be turned {\sl off} specifically as it is {\sl on} by default.}
+\exstep{Open a sequence alignment, for example the PFAM domain PF03460 in PFAM
+seed database. Select the alignment menu option {\sl Colour $\Rightarrow$
+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}. Select a group
of around 4 similar sequences. Use the context menu (right click on the group)
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
-colouring schemes like Blosum62 are based on the group being coloured, not the
-whole alignment (this also explains the colouring changes observed in exercise
-\ref{exselect} during the group selection step).
-}
-\exstep{
-Keeping the same selection as before, colour the complete alignment except
+colouring schemes like Blosum62 are based on the selected group,
+not the whole alignment (this also explains the colouring changes observed in exercise
+\ref{exselect} during the group selection step).}
+\exstep{Keeping the same selection as before, colour the complete alignment except
the group using {\sl Colour $\Rightarrow$ Taylor}.
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
-Slide the selector from side to side and observe the changes in the alignment colouring in the selection and in the complete alignment.
-}
+Slide the selector from side to side and observe the changes in the alignment
+colouring in the selection and in the complete alignment.}
+{\bf A video about this exercise is available on the Jalview website
+at \url{http://www.jalview.org/training/Training-Videos}.}
}
\subsubsection{User Defined}
\exercise{User Defined Colour Schemes}{
-\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialogue window will open.
-}
-\exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.
-}
-\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialogue window can now be closed.
-}
-\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.
-}
-}
+\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialogue window will open.}
+\exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.}
+\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialogue window can now be closed.}
+\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 A video about this exercise is available on the Jalview website at at
+\url{http://www.jalview.org/training/Training-Videos}.}} }
\section{Formatting and Graphics Output}
\label{layoutandoutput}
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. }
-\exstep{Hide all the annotation rows by selecting {\sl Annotations $\Rightarrow$
+\exstep{Hide all the annotation rows by toggling {\sl Annotations $\Rightarrow$
Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.} \exstep{Deselect {\sl Format $\Rightarrow$ Wrap}. Right click on the
-annotation row labels to bring up the pop-up context menu, then select {\sl
-Hide This Row}. Bring up the pop-up context menu again and select {\sl
+annotation row labels to bring up the context menu, then select {\sl
+Hide This Row}. Bring up the context menu again and select {\sl
Show All Hidden Rows} to reveal them.}
-\exstep{Annotations can be reordered by clicking and dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot} below.}
-\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label -
+\exstep{Annotations can be reordered by clicking and dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just
+above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot}.}
+\exstep{Move the mouse to the top left hand corner of the annotation labels -
a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed
-by clicking and dragging the mouse up or down.}
+by clicking and dragging this icon up or down.}
}
\subsection{Graphical Output}
For submission of alignment figures to journals, please use EPS\footnote{If the journal complains, {\em insist}.}.
}
\parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_png.pdf}} \par \centerline{Zoom Detail of PNG image.}}
+
\exercise{Graphical Output}{
\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}.
Customise it how you wish but leave it unwrapped.
alignment window but {\bf annotations are not exported}).}
\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ PNG} menu option.
Open the file in an image viewer that allows zooming such as Paint or Photoshop (Windows), or Preview (Mac OS X) and zoom in.
-Notice that the image is a bitmap and it becomes pixelated very quickly.
+Notice that the image is a bitmap and it becomes pixelated when zoomed.
(Note that the {\bf annotation lines are included} in the image.)}
\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image
$\Rightarrow$ EPS} menu option. Open the file in a suitable program such as
G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}.
Consensus is the modal residue (or {\tt +} where there is an equal top residue).
The inclusion of gaps in the consensus calculation can be toggled by
-right-clicking on the the Consensus label and selecting {\sl Ignore Gaps in
+right-clicking on the Consensus label and selecting {\sl Ignore Gaps in
Consensus} from the pop-up context menu located with consensus annotation row.
Quality is a measure of the inverse likelihood of unfavourable mutations in the alignment. Further details on these
calculations can be found in the on-line documentation.
\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
Right-click on the {\sl Conservation} annotation row to
bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}.
-Enter ``Iron binding site" and click OK. A new, empty, row appears.
+Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
}
\exstep{
Navigate to column 97. Move down and on the new annotation row called
``Iron binding site, select column 97.
Right click at this selection and select {\sl Label} from the context menu.
-Enter ``Fe" in the box and click OK. Right-click on the selection again and select {\sl Colour}.
+Enter ``Fe" in the box and click {\sl OK}. Right-click on the selection again
+and select {\sl Colour}.
Choose a colour from the colour chooser dialogue
-and click OK. Press [ESC] to remove the selection.
+and click {\sl OK}. Press [ESC] to remove the selection.
}
\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the
context menu. You will be prompted for a label. Enter ``B" and press OK. A new line showing the
arrow.
}
\exstep{Right click on the title text of annotation row that you just created.
-Select {\sl Export Annotation} and, in the {\bf Export Annotation} dialog box that will open, select the Jalview format and click
+Select {\sl Export Annotation} and, in the Export Annotation dialog box that will open, select the Jalview format and click
the [To Textbox] button.
The format for this file is given in the Jalview help. Press [F1] to open it, and find
row. Save the file and drag it onto the alignment view.}
\exstep{Try to add an additional helix somewhere along the row by editing the file and
re-importing it.
-{\sl Hint: Use the {\bf Export Annotation} function to view what helix annotation looks like in
+{\sl Hint: Use the Export Annotation function to view what helix annotation looks like in
a Jalview annotation file.}}
\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...}
function to export all the alignment's annotation to a file.}
-\exstep{Open the exported annotation in a text editor, and use the {\bf Annotation File Format}
+\exstep{Open the exported annotation in a text editor, and use the Annotation File Format
documentation to modify the style of the Conservation, Consensus and Quality annotation rows so
they appear as several lines on a single line graph.
{\sl Hint: You need to change the style of annotation row in the first field of the annotation
\label{viewannotfileex}\exstep{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. Note the
-{\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the
+SEQUENCE\_REF statements surrounding the row specifying the sequence association for the
annotation. } }
\exstep{Once the process has finished, save the alignment as a Jalview Project.}
\exstep{Now close all the windows and open the project again, and verify that the database references and sequence features are still present on the alignment}
-\exstep{View the {\sl Sequence details \ldots} report for the FER1\_SPIOL sequence and for the whole alignment. Which sequences have web links associated with them ?}
+\exstep{View the {\sl Sequence details \ldots} report for the FER1\_SPIOL sequence and for the whole alignment. Which sequences have web links associated with them?}
}
\exstep{
Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
appropriate box. Click on the Feature Colour bar to change the colour if
-desired, add a short description (``One of four Iron binding Cysteines") and press OK. The features will then appear on the sequences. } \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] then insert a gap in sequence 3 at column 95. Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
+desired, add a short description (``One of four Iron binding Cysteines") and
+press {\sl OK}. The features will then appear on the sequences. } \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] then insert a gap in sequence 3 at column 95.
+Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
}
\exstep{
Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature
this so that you can see the features you have just created. Click the check
box for ``Iron binding site" under {\sl Display} and note that display of this
feature type is now turned off. Click it again and note that the features are
-now displayed. Close the sequence feature settings box by clicking OK or
-Cancel.} }
+now displayed. Close the sequence feature settings box by clicking {\sl OK} or
+{\sl Cancel}.} }
\chapter{Multiple Sequence Alignment}
\label{msaservices}
A window will open giving the job status. After a short time, a second window will open
with the results of the alignment.}
\exstep{Return to the first sequence alignment window by clicking on
- the window, and repeat using ClustalO (Omega) and MAFFT (from the {\sl Web
- Service $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and
+ the window, and repeat using {\sl ClustalO} (Omega) and {\sl MAFFT} (from the
+ {\sl Web Service $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and
you should notice small differences. }
\exstep{Select the last three sequences in the MAFFT alignment, and de-align them
with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect these
-sequecnes. Then submit this view for re-alignment with ClustalO.}
-\exstep{Return to the window in section (c), use [CTRL]-Z (undo) to recover the
-alignment of the last three sequences in this MAFFT alignment.
+sequences. Then submit this view for re-alignment with {\sl ClustalO}.}
+\exstep{Return to the alignment window in section (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.}
\exstep{Select columns 60 to 125 in the original MAFFT alignment and hide them,
\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
-the calculation finishes, a 3D viewer displays the each sequence as a point in
+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.
Note: The calculation is computationally expensive, and may fail for very large
\subsubsection{The PCA Viewer}
-PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principlal
+PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principal
Component Analysis} menu option. {\bf PCA requires a selection containing at
least 4 sequences}. A window opens containing the PCA tool (Figure \ref{PCA}).
Each sequence is represented by a small square, coloured by the background
\exercise{Principal Component Analysis}
{ \exstep{Load the alignment at
-\textsf{http://www.jalview.org/tutorial/alignment.fa} }
+\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}.
-A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible.
+A new window will open. Move this window within the desktop so that the tree,
+alignment and PCA viewer windows are all visible.
Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window.
Note that clicking on points in the plot will highlight them on the alignment. }
\exstep{ Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
Neighbour Joining Using BLOSUM62}. A new tree window will appear.
-Click on the tree window. Careful selection of the tree partition location will divide the alignment into a number of groups,
-each of a different colour.
+Place the mouse cursor on the tree window so that the
+tree partition location will divide the alignment into a number of groups, each of a different colour.
Note how the colour of the sequence ID label matches both the colour of
the partitioned tree and the points in the PCA plot.} }
Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
can help when working with larger alignments.
-\exercise{Trees}{
-\exstep{Ensure that you have at least 1G memory available in Jalview
+\exercise{Trees}
+{Ensure that you have at least 1G memory available in Jalview
(Either start with this link:
\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
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 ``latest official build'' row in the table, go to the
-``Webstart'' column, click on ``G2''.)}
+``Webstart'' column, click on ``G2''.)
+
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
-\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour.
-Place the cursor to give about 4 groups. In the alignment window, select
+\exstep{Click on the tree window, a cursor will appear. Note that placing
+this cursor divides the tree into a number of groups by colour.
+Place the cursor to give about 4 groups.}
+\exstep{In the alignment window, select
{\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are
reordered to match the order in the tree and groups are formed implicitly.
Alternatively in the tree window, select {\sl View $\Rightarrow$ Sort Alignment
by Tree}.} \exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree
$\Rightarrow$ Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring makes it easy to see the differences between the two trees, calculated using
different methods.} \exstep{Select from sequence 2 column 60 to sequence 12 column 123. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear. It can be seen that the tree contains 11 sequences. It has been coloured according to the already selected groups from the first tree and is calculated purely from the residues in the selection.
+
Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the
alignment for the calculation of trees. }}
-\exercise{Pad Gaps in Alignment}{
-\exstep{Recover the {\sl Input Data} for the tree you just calculated from the
-{\sl File} menu. In alignment window, ensure that the {\sl Edit $\Rightarrow$
+\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
alignment.}
\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
gaps ensures all the sequences are the same length after editing.
{\sl Pad Gaps } option
-can also be set using
+can be set in Preferences using
{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}. }
}
\exstep{Build a Neighbour joining tree using Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
Neighbour Joining Using BLOSUM62}.}
\exstep{Use the mouse cursor to select a point on the tree to partition the
-alignment}
-\exstep {{\sl Sort Alignment By Tree} option in the tree viewer submenu to
-re-order the sequences in the alignment using the calculated tree. Examine the
-variation in colouring between different groups of sequences in the alignment
-window.
-
-You may find it easier to browse the alignment if you first uncheck the {\sl
-Annotations $\Rightarrow$ Show Annotations} option, and open the Overview Window
+alignment into several sections.}
+\exstep {Select {\sl View $\Rightarrow$ Sort Alignment By Tree} option in the
+tree window to re-order the sequences in the alignment using the calculated
+tree.
+Examine the variation in colouring between different groups of sequences in the alignment
+window.}
+
+\exstep {You may find it easier to browse the alignment if you first uncheck the
+{\sl Annotations $\Rightarrow$ Show Annotations} option, and open the Overview Window
within the View menu to aid navigation.}
\exstep{Try changing the colourscheme of the residues in the alignment to
\exercise{Remove Redundant Sequences}{
-\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc}). In
-the alignment window, you may need to deselect groups using Esc key.}
+\exstep{Using the alignment generated in the previous exercise (exercise
+\ref{consanalyexerc}).
+In the alignment window, you may need to deselect groups using Esc key.}
\exstep{In the {\sl Edit} menu select {\sl Remove Redundancy} to open the
Redundancy threshold selection dialog. Adjust the redundancy threshold value, start
\exercise{Group Conservation Analysis}{
\exstep{Re-use or recreate the alignment and tree which you worked with in the
tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
-\exstep{In the {\sl View} menu, select {\sl New View} to create a new
-view. Ensure the annotation panel is displayed ({\sl Show annotation} in {\sl Annotations} menu). Enable the
+\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 Show annotation} in {\sl Annotations} menu). Enable the
display of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
Autocalculated Annotation } submenu in the sequence alignment window.}
\exstep{Displaying the sequence
open the context menu and select the {\sl Show Logo} option.}
\exstep{In the column alignment ruler, select a column exhibiting about 50\%
conservation that lies within the central conserved region of the alignment.
-(Column 74 is used in the Tree video).}
+(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{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 { ok}.
+opens a Structure Chooser window, select { \sl 1A70} and click {\sl OK}.
{\sl Note: the Structure Chooser interface
provides a smart technique for selecting PDB structures by queryingthe meta-data
Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. }
\exstep{In the structure viewer menu, select {\sl Colours $\Rightarrow$ Background
Colour\ldots} and choose a suitable colour.
-Press OK to apply this.}
+Press {\sl OK} to apply this.}
\exstep{Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the
image. On your computer, view this with a suitable program. }
\exstep{Select
\exstep{Close the Jalview program, from the
{\sl Desktop menu} select {\sl Jalview $\Rightarrow$ Quit Jalview}. Then reopen
Jalview, Chimera should open as the default viewer.}
-{\s Note: The Jmol structure viewer sits within the Jalview desktop; however the Chimera structure viewer
-sits outside the Jalview desktop and a Chimera
+{\sl Note: The Jmol structure viewer sits within the Jalview desktop; however
+the Chimera structure viewer sits outside the Jalview desktop and a Chimera
view window sits inside the Jalview desktop.} }
\subsection{Superimposing Structures}
biochemical properties of a given molecule are significantly different to its
homologues. When structure data is available, comparing the shapes of molecules
by superimposing them enables substructure that may impart different behaviour
-to be quickly identified. The identification of optimal 3D superpositions
+to be quickly identified. The identification of optimal 3D superposition
involves aligning 3D data rather than sequence symbols, but the result can
still be represented as a sequence alignment, where columns indicate positions
in each molecule that should be superposed to recreate the optimal 3D alignment.
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 outputed to the Jalview
+Full information about the superposition is also outputted to 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.
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 {\bf Yes} button.
+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
moved on to the other. If this doesn't happen, use the Align function in the Jmol submenu}}
{\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. (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
+the small section 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 ?} }
\subsubsection{Colouring Complexes}
}
\exstep{
Select the sequence used in the second sequence prediction by clicking on its
-name in the sequence ID panel, and copy {\sl (CTRL or Command + C)} and then
-paste it {\sl (CTRL or Command + V)} into the first prediction window. You
+name in the sequence ID panel, and copy {\sl ([CTRL] or [CMD]-C)} and then
+paste it {\sl [CTRL] or [CMD]-V)} into the first prediction window. You
can now compare the two predictions as the annotations associated with the
sequence has also been copied across.
% which is described in Section \ref{seqassocannot} below.
values are structured.
{\bf Disordered region} sequence features are created marking mark range(s) of residues with positive first order derivatives, and
-\textbf{Globular Domain} features mark long stretches of order. \textbf{Dydx} annotation rows gives the first order derivative of smoothed score. Values above 0 indicates
+\textbf{Globular Domain} features mark long stretches of order. \textbf{Dydx} annotation rows give the first order derivative of smoothed score. Values above 0 indicates
residue is disordered.
\textbf{Smoothed Score and Raw Score} annotation rows give the smoothed and raw scores used to create the differential signal that
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.}}
+the structures for all sequences. {\sl Hint: see \ref{viewAllStructures} to see
+how to do this.}}
\exstep{Compare the disorder predictions to the structure data by mapping any
available temperature factors to the alignment {\sl via} the {\sl Sequence ID
Popup $\Rightarrow$ Selection $\Rightarrow$ Add reference annotation} option.}
-\exstep{Apply the IUPred disorder prediction method}
+\exstep{Apply the IUPred disorder prediction method.}
\exstep{Use the {\sl Per
sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog to shade
the sequences by the long and short disorder predictors.
git://source.jalview.org / jalview-manual.git / commitdiff