\vspace{0.5in}
{\huge
-Manual and Introductory Tutorial }
+Manual and Introductory Tutorial }
\vspace{2.4in}
\vspace{2in}
-Manual Version 1.5
+Manual Version 1.5.1
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-4th December 2014
+24th April 2015
\end{center}
desktop's webservice and figure generation capabilities. It is designed to be
embedded in a web page,\footnote{A demonstration version of Jalview (Jalview Micro
Edition) also runs on a mobile phone but the functionality is limited to sequence
-colouring.} and includes a javascript API to allow customisable display of alignments for web sites such as
-{\bf Pfam}.\footnote{\url{http://pfam.xfam.org}}
+colouring.} and includes a javascript API to allow customisable display of
+alignments for web sites such as Pfam.\footnote{\url{http://pfam.xfam.org}}
Jalview 2.8.2 was released in December 2014. The Jalview Desktop in this version
\end{figure}
-\exercise{Launching Jalview from the Jalview website}{
+\exercise{Launching Jalview from the Jalview Website}{
\label{start}
\exstep{Open the Jalview web
site \href{http://www.jalview.org}{(www.jalview.org)}
\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, selected exampleFile-2-7.jar, then click OK.}
+files, select exampleFile\_2\_7.jar, then click OK.}
{\bf Note:} Should you want to reload the example alignment or load your own
sequence during the launch process, then go
to the {\sl Tools $\Rightarrow$
may want to move this from the downloads folder to another folder.
Opening from this file will allow Jalview to be launched offline.
-{\bf Help launching Jalview is available in a video on
-\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
-the website.}}
+{\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}.}}
\subsection{Getting Help}
\label{gettinghelp}
-\subsubsection{Built in documentation}
+\subsubsection{Built in Documentation}
Jalview has comprehensive on-line help documentation. Select {\sl Help
$\Rightarrow$ Documentation} from the main window menu and a new window will
open (Figure \ref{help}). The appropriate topic can then be selected from the
\end{center}
\end{figure}
-\subsubsection{Email lists}
+\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
Rapid movement to specific positions is accomplished as listed below:
\begin{list}{$\circ$}{}
-\item {\bf Jump to Sequence {\sl n}:} Type a number {\sl n} then press [S] to move to sequence (row) {\sl n}
+\item {\bf Jump to Sequence {\sl n}:} Type a number {\sl n} then press [S] to
+move to sequence (row). {\sl n}
\item {\bf Jump to Column {\sl n}:} Type a number {\sl n} then press [C] to move to column {\sl n} in the alignment.
\item {\bf Jump to Residue {\sl n}:} Type a number {\sl n} then press [P] to move to residue number {\sl n} in the current sequence.
\item {\bf Jump to column {\sl m} row {\sl n}:} Type the column number {\sl m}, a comma, the row number {\sl n} and press [RETURN].
\exstep{Find the Overview Window, {\sl Views
$\Rightarrow$ Overview Window} and open it. Move around the
alignment by clicking and dragging the red box in the overview window.}
-\exstep{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
+\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] to enter {\bf Cursor mode}. Use the direction {\bfarrow
-keys} to move the cursor around the alignment.}
+\exstep{Press [F2] key (or [Fn]/[F2] on Mac) to enter {\bf Cursor mode}. Use
+the direction {\bfarrow 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,
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 Jalview is available in a video on
-\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
-the website.}}
+{\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}.}}
\subsection{The Find Dialog Box}
\label{searchfunction}
\end{figure}
-\exercise{Loading sequences}{
+\exercise{Loading Sequences}{
\label{load}
\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
close all windows.}
{\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.
-
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.
sources.
Select the {\bf PFAM seed} database and click ok, then enter the accession
-number {\bf PF03460} and click OK. An alignment of about 107 sequences should load.
+number {\bf PF03460} and click 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
-or accession numbers can be loaded by using semicolons to separate them.}}
+or accession numbers 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}.}
+}
\subsection{Memory Limits}
\label{memorylimits}
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. } }
+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}.}}
\section{Selecting and Editing Sequences}
To define a selection in cursor mode (which is enabled by pressing [F2] when the alignment window is selected),
navigate to the top left corner of the proposed selection (using the mouse, the arrow keys, or the keystroke
commands described in Section \ref{cursormode}). Pressing the [Q] key marks this as the
-corner. A red outline appears around the cursor (Figure \ref{cselect})
+corner. A red outline appears around the cursor (Figure \ref{cselect}).
Navigate to the bottom right corner of the proposed selection and press the [M] key. This marks the bottom right corner of the selection. The selection can then be treated in the same way as if it had been created in normal mode.
This may also be useful when hiding large regions in an alignment (see Section \ref{hidingregions} below).
Instead of selecting the columns and rows that are to be hidden, simply select the region that is to be kept
visible, invert the selection, then select {\sl View $\Rightarrow$ Hide
-$\Rightarrow$ Selected Region }.
+$\Rightarrow$ Selected Region}.
\subsection{Creating Groups}
Selections are lost as soon as a different region is selected. Groups can be
\exercise{Making Selections and Groups}{
\label{exselect}
-\exstep{Close all windows in Jalview.
-Load the ferredoxin alignment (PFAM
-ID PF03460 from PFAM seed database).
+\exstep{Close windows.
+Load the ferredoxin alignment (PF03460 from PFAM seed database).
Choose a residue and place the mouse
-cursor on it. Note residue information will show in alignment window status bar.
-Click and drag the mouse cursor to create a selection. As you drag, a red box
+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.
Release the mouse
-button and a red box should border the selected region.
-Press [ESC] to clear the selection.}
+button and a red box borders the selected region.
+Press [ESC] to clear this.}
\exstep{ Select one sequence by clicking on
the sequence ID panel. Note that the sequence ID takes on a highlighted
background and a red box appears around the selected sequence.
Hold down [SHIFT] and click another sequence ID a few positions above or below.
Note how the selection expands to include all the sequences between the two positions on which you clicked.
-
Hold down [CTRL] and then click on several sequences ID's both selected and
unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are
individually deselected.}
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
-to include newly selected sequences, and the `Percentage Identity' colouring changes. } \exstep{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
+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
+the right-hand edge of the selected group.}
\exstep{The current selection can be {\bf exported} and saved by right clicking
on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an
\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}.}
% more? change colouring style. set border colour.
}
\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.} }
+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}.}}
\subsection{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}{
+\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
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
with (Sequence ID name )}. To reveal these hidden sequences, right click on the
-Sequence ID and in the pop-up menu select Reveal All.}}
+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}}}
+
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit1.pdf}
+\includegraphics[width=3in]{images/edit2.pdf}
+\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
+selected sequence is dragged to the right while pressing and holding [SHIFT].}
+\label{gapseq}
+\end{center}
+\end{figure}
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit3.pdf}
+\includegraphics[width=3in]{images/edit4.pdf}
+\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
+group is dragged to the right with [CTRL] pressed.}
+\label{gapgroup}
+\end{center}
+\end{figure}
\subsubsection{Introducing Gaps in a Single Sequence}
-To introduce a gap, place the cursor on the residue to the immediate right of
-where the gap should appear. Hold down the SHIFT key and the left mouse button,
-then drag the sequence to the right until the required number of gaps has been inserted.
+To introduce a gap, first select the sequence in the sequence ID panel and
+then place the cursor on the residue to the immediate right of where the gap
+should appear. Hold down the SHIFT key and the left mouse button, then drag the sequence to the right until the required number of gaps has been inserted.
One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long. Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
\subsubsection{Introducing Gaps in all Sequences of a Group}
-To insert gaps in all sequences in a selection or group, place the mouse cursor on any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the CTRL key and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
+To insert gaps in all sequences in a selection or group, select the
+required sequences in the sequence ID panel and then place the mouse cursor on
+any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the CTRL key and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
Gaps can be removed by dragging the residue to the immediate right of the gap
leftwards whilst holding down [SHIFT] (for single sequences) or [CTRL] (for a group of sequences).
\subsubsection{Sliding Sequences}
Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
-sequences are selected will ``slide'' the selected sequences to the left or
-right (respectively). Slides occur regardless of the region selection -
+sequences are selected will ``slide'' the entire selected sequences to the left
+or right (respectively). Slides occur regardless of the region selection -
which, for example, allows you to easily reposition misaligned subfamilies
within a larger alignment.
Sequences}). }
\exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
-the left so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
+the right so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
\exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
O80429\_MAIZE
}
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit1.pdf}
-\includegraphics[width=3in]{images/edit2.pdf}
-\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
-selected sequence is dragged to the right while pressing and holding [SHIFT].}
-\label{gapseq}
-\end{center}
-\end{figure}
-
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit3.pdf}
-\includegraphics[width=3in]{images/edit4.pdf}
-\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
-group is dragged to the right with [CTRL] pressed.}
-\label{gapgroup}
-\end{center}
-\end{figure}
-
-
\subsubsection{Editing in Cursor mode}
Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
\ref{mousealedit}, and recreates the final part of the example ferredoxin
alignment from the unaligned sequences using Jalview's keyboard editing mode.
-{\bf {\sl Note for Windows Users:}} The [SHIFT]-[SPACE] command has the same effect as
-the [CTRL]-[SPACE] command mentioned in this exercise, and you should use
-[SHIFT]-[SPACE] in order to avoid opening the window menu.}
+{{\bf Note:}} For Mac users, [CTRL]-[SPACE] command
+has the same effect as the [SHIFT]-[SPACE] command mentioned in this exercise.
+
+Window users should use [SHIFT]-[SPACE] rather than the [CTRL]-[SPACE] command,
+as this command will close the window.}
\exstep{Load the sequence alignment at
\textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the
Now, enter cursor mode by pressing [F2]}
% TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783
\exstep{Insert 58 gaps at the start of the first sequence (FER\_CAPAA). Press {\sl 58} then {\sl [SPACE]}. }
-\exstep{Go down one sequence and select rows 2-5 as a block. Click on the second sequence ID (FER\_CAPAN). Hold down shift and click on the fifth (FER1\_PEA). }
+\exstep{Go down one sequence and select rows 2-5 as a block. Click on the second sequence ID (FER\_CAPAN).
+ Hold down shift and click on the fifth (FER1\_PEA). }
\exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing
{\sl 1,2} then press {\sl [RETURN]}. Now insert 6 gaps in all the sequences.
-Type {\sl 6} then hold down {\sl [CTRL]} and press {\sl [SPACE]}.} \exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47.
-Press {\sl 34C} then {\sl [CTRL]-[SPACE]}. Press {\sl 38C} then [CTRL]-[SPACE].
-Press {\sl 47C} then {\sl 3 [CTRL-SPACE]} the first through fourth sequences are
-now aligned.}
+Type {\sl 6} then hold down {\sl [SHIFT]} and press {\sl [SPACE]}.}
+\exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47.
+Press {\sl 34C} then {\sl [SHIFT]-[SPACE]}. Press {\sl 38C} then
+[SHIFT]-[SPACE].
+Press {\sl 47C} then {\sl 3 [SHIFT-SPACE]} the first through fourth sequences
+are now aligned.}
\exstep{The fifth sequence (FER1\_PEA) is poorly aligned. We will delete some gaps and add some new ones. Press {\sl [ESC]} to clear the selection. Navigate to the start of sequence 5 and delete 3 gaps. Press {\sl 1,5 [RETURN]} then {\sl 3 [BACKSPACE]} to delete three gaps. Go to column 31 and delete the gap. Press {\sl 31C [BACKSPACE]} .}
\exstep{ Similarly delete the gap now at column 34, then insert two gaps at column 38. Press {\sl 34C [BACKSPACE] 38C 2 [SPACE]}. Delete three gaps at column 44 and insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are now aligned.}
}
\subsubsection{Taylor}
\parbox[c]{3.5in}{
-This colour scheme was devised by Willie Taylor and an entertaining description of it's origin can be found in Protein Engineering, Vol 10 , 743-746 (1997)
+This colour scheme was devised by Willie Taylor and an entertaining description of its origin can be found in Protein Engineering,
+Vol 10 , 743-746 (1997).
}
\parbox[c]{3in}{
\includegraphics[width=2.75in]{images/col_taylor.pdf}
\parbox[c]{3.5in}{ Residues are coloured according to whether the corresponding
nucleotide bases are purine (magenta) or pyrimidine (cyan) based. All non ACTG
residues are uncoloured. For further information about working with nucleic acid
-sequences and alignments, see Section \ref{workingwithnuc}
+sequences and alignments, see Section \ref{workingwithnuc}.
%and Section \ref{workingwithrna}
-.
} \parbox[c]{3in}{ \includegraphics[width=2.75in]{images/col_purpyr.pdf} }
-\subsubsection{RNA Helix colouring}
+\subsubsection{RNA Helix Colouring}
\parbox[c]{3.5in}{ Columns are coloured according to their assigned RNA helix as
defined by a secondary structure annotation line on the alignment. Colours for
each helix are randomly assigned, and option only available when an RNA
\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 $\Rightarrow$ Group $\Rightarrow$ Group Colour
+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
\ref{exselect} during the group selection step).
}
\exstep{
-Keeping the same selection as before, colour the complete alignment 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.
+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.
}
}
\end{figure}
-\exercise{User defined colour schemes}{
+\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.
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 View $\Rightarrow$ 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
+\exstep{Hide all the annotation rows by selecting {\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
Show All Hidden Rows} to reveal them.}
available to Jalview users, and Section \ref{jabaservices} explains how to
configure the Jalview Desktop for access to new JABAWS servers.
Section \ref{msaservices} describes how to use the range of multiple alignment
-programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS' AACon
+programs provided by JABAWS, and Section \ref{aacons} introduces JABAWS AACon
service for protein multiple alignment conservation analysis.
Section \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS' protein disorder prediction
+structure predictions with JPred, and JABAWS protein disorder prediction
services are introduced in Section \ref{protdisorderpred}.
Section \ref{featannot} describes the mechanisms provided by Jalview for
% and Section \ref{workingwithrna} covers the visualization,
% editing and analysis of RNA secondary structure.
-\section{Working with structures}
+\section{Working with Structures}
\label{wkwithstructure}
Jalview facilitates the use of protein structures for the analysis of alignments
by providing a linked view of structures associated with sequences in
the European Protein Databank (PDBe) using the Sequence Fetcher (see
\ref{fetchseq}).
-\subsection{Automatic association of PDB structures with sequences}
+\subsection{Automatic Association of PDB Structures with Sequences}
Jalview can automatically determine which structures are associated with a
sequence in a number of ways.
-\subsubsection{Discovery of PDB IDs from sequence database cross-references}
+\subsubsection{Discovery of PDB IDs from Sequence Database Cross-references}
If a sequence has an ID from a public database that contains cross-references to
the PDB, such as Uniprot. Right-click on any sequence ID and select {\sl Structure $\Rightarrow$
Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (Figure \ref{auto}). Jalview will attempt to associate the
}
}
-\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence. After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and any associated PDB structures (right)}
+\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence.
+After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and
+any associated PDB structures (right).}
\label{auto}
\end{center}
\end{figure}
-\subsubsection{Drag-and-drop association of PDB files with sequences by filename
-match}
+\subsubsection{Drag-and-Drop Association of PDB Files with Sequences by Filename
+Match}
\label{multipdbfileassoc}
If one or more PDB files stored on your computer are dragged from their location
on the file browser onto an alignment window, Jalview will search the alignment
If no associations are made, then sequences extracted
from the structure will be simply added to the alignment. However, if only
-some of the PDB files are associated, jalview will raise another dialog box giving
-you the option to add any remaining sequences from the PDB structure files not present in
+some of the PDB files are associated, Jalview will raise another dialog box
+giving you the option to add any remaining sequences from the PDB structure files not present in
the alignment. This allows you to easily decorate sequences in a newly imported
alignment with any corresponding structures you've already collected in a directory
accessible from your computer.\footnote{We plan to extend this facility in
\end{center}
\end{figure}
-\subsection{Customising structure display}
+\subsection{Customising Structure Display}
Structure display can be modified using the {\sl Colour} and {\sl View} menus
in the structure viewer. The background colour can be modified by selecting the
sequence (How well and which parts of the structure relate to the sequence) can
be viewed with the {\sl File $\Rightarrow$ View Mapping} menu option.
-\subsubsection{Using the Jmol visualization interface }
+\subsubsection{Using the Jmol Visualization Interface }
Jmol has a comprehensive set of selection and visualization functions that are
accessed from the Jmol popup menu (by right-clicking in the Jmol window or by
\exercise{Viewing Structures}{\label{viewingstructex}
\exstep{Load the alignment at
\textsf{http://www.jalview.org/examples/exampleFile.jar}. Right-click on the
-sequence ID label for any of the sequences (e.g. {\sl FER1\_SPIOL}) to bring up
+sequence ID label of {\sl FER1\_SPIOL}, this brings up
the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$
Associate Structure with Sequence $\Rightarrow$ Discover
PDB IDs}. Jalview will now attempt to find PDB structures for the sequences in
\exstep{Select {\sl File $\Rightarrow$ View Mapping} from the structure viewer menu. A new window opens showing the residue by residue alignment between the sequence and the structure.}
\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file. Once the file is saved, open the location in your file browser (or explorer window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu). Verify that you can open and view the associated structure from the sequence ID pop-up menu's {\sl Structure } submenu in the new alignment window.}
-\exstep{Right click on the structure to bring up the Jmol window. Explore the menu options. Try to change the style of molecular display - by first using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.}
-\exstep{Use the {\sl File $\Rightarrow$ Save As .. } function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
+\exstep{Right click on the structure in the submenu and bring up the Jmol
+window.
+Explore the menu options. Try to change the style of molecular display - by first using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.} \exstep{Use the {\sl File $\Rightarrow$ Save As .. } function to save the alignment as a Jalview Project. 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.}
}
-\subsection{Superimposing structures}
+\subsection{Superimposing Structures}
\label{superposestructs}
Many comparative biomolecular analysis investigations aim to determine if the
biochemical properties of a given molecule are significantly different to its
$>$ 1) if the current selection contains two or more sequences with associated
structures.
-\subsubsection{Obtaining the RMSD for a superposition}
+\subsubsection{Obtaining the RMSD for a Superposition}
The RMSD (Root Mean Square Deviation) is a measure of how similar the structures
are when they are superimposed. Figure \ref{mstrucsuperposition} shows a
superposition created during the course of Exercise \ref{superpositionex}. The
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 output to the Jalview
+Full information about the superposition is also outputed 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.
-\subsubsection{Choosing which part of the alignment is used for structural
-superposition} Jalview uses the visible part of each alignment view to define
+\subsubsection{Choosing which part of the Alignment is used for Structural
+Superposition} Jalview uses the visible part of each alignment view to define
which parts of each molecule are to be superimposed. Hiding a column in a view
used for superposition will remove that correspondence from the set, and will
exclude it from the superposition and RMSD calculation.
\begin{center}
\includegraphics[width=5.5in]{images/fdxsuperposition.pdf}
\caption{{\bf Superposition of two ferredoxin structures.} The alignment on the
-left was used by jalview to superpose structures associated with the
+left was used by Jalview to superpose structures associated with the
FER1\_SPIOL and FER1\_MAIZE sequences in the alignment. Parts of each structure
used for superposition are rendered as a cartoon, the remainder rendered in
wireframe. The RMSD between corresponding positions in the structures before and
\end{center}
\end{figure}
-\exercise{Aligning structures using the ferredoxin
-sequence alignment.}{\label{superpositionex}
+\exercise{Aligning Structures using the Ferredoxin
+Sequence Alignment}{\label{superpositionex}
\exstep{Continue with the Jalview project created in exercise
\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
IDs associated with the FER1\_MAIZE sequence.}
\exstep{Once discovery has completed, use the {\sl
-View PDB Structure} submenu to view the PDB file associated with FER1\_MAIZE.
+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.
\exstep{Create a new view on the alignment, and hide all but columns 121
through to 132.}
\exstep{Use the {\sl Jmol} submenu to
-recompute the superposition using just columns 121-132 of the alignment.
+recompute the superposition using just columns 121-132 of the alignment
+(The easiest way to achieve this is to select column 121-132 and in the View
+menu selected ``All but selected region'' from the Hide options).
{\sl Note how the molecules shift position when superposed using a short part of
the two structures.}}
\exstep{Compare the initial and final RMSDs for superimposing molecules with
-the small section and with the whole alignment. Which view do you think give the
-best 3D superposition, and why ?} }
+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
+superposition, and why ?} }
-\subsection{Colouring structure data associated with multiple alignments and views}
-Normally, the original view from which a particular structure view was
+\subsection{Colouring Structure Data Associated with Multiple Alignments and
+Views} Normally, the original view from which a particular structure view was
opened will be the one used to colour structure data. If alignments involving
sequences associated with structure data shown in a Jmol have multiple views, Jalview gives you full control
over which alignment, or alignment view, is used to colour the structure
\end{center}
\end{figure}
-\subsubsection{Colouring complexes}
+\subsubsection{Colouring Complexes}
\label{complexstructurecolours}
The ability to control which multiple alignment view is used to colour
structural data is essential when working with data relating to
evolutionary history, and a complete picture of functional variation can
only be gained by integrating data from different alignments on the same
structure view. An example of this is shown in Figure
-\ref{mviewalcomplex}, based on data from Song et. al\footnote{Structure of
+\ref{mviewalcomplex}, based on data from Song et. al.\footnote{Structure of
DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation. Jikui Song, Olga Rechkoblit, Timothy H. Bestor, and Dinshaw J. Patel.
{\sl Science} 2011 {\bf 331} 1036-1040
\href{http://www.sciencemag.org/content/331/6020/1036}{DOI:10.1126/science.1195380}}
\end{center}
\end{figure}
-\exercise{Colouring a protein complex to explore domain-domain interfaces}{\label{dnmtcomplexex}
+\exercise{Colouring a Protein Complex to Explore Domain-Domain
+Interfaces}{\label{dnmtcomplexex}
\exstep{Download the PDB file at
\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop.
{\sl Use the following webstart link:
-\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}}
-\exstep{Retrieve the following
-{\bf full} PFAM alignments: PF02008, PF00145, PF01426 (make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.}
-\exstep{Drag the structure you downloaded in
+\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}
+
+{\sl Alternatively in the Development section of the Jalview web site
+(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds})
+in the ``latest official build'' row in the table, go to the
+``Webstart'' column, click on ``G2''.}}
+\exstep{Retrieve the following {\bf full} PFAM alignments: PF02008, PF01426
+(make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.} \exstep{Drag the URL or file of the structure you downloaded in
step 1 onto one of the alignments to associate it with the mouse sequence in
that Pfam domain family.}
\exstep{For every DNMT1\_MOUSE sequence in the alignment, use the sequence
% for one relating to highlighting of positions in the alignment window).}
}
-\section{Analysis of alignments}
+\section{Analysis of Alignments}
\label{alignanalysis}
Jalview provides support for sequence analysis in two ways. A number of
analytical methods are `built-in', these are accessed from the {\sl Calculate}
\begin{center}
\includegraphics[width=2in]{images/PCA1.pdf}
\includegraphics[width=3in]{images/PCA3.pdf}
-\caption{{\bf PCA Analysis} }
+\caption{{\bf PCA Analysis.} }
\label{PCA}
\end{center}
\end{figure}
the partitioned tree and the points in the PCA plot.
} }
-\subsubsection{PCA data export}
+\subsubsection{PCA Data Export}
Although the PCA viewer supports export of the current view, the plots produced
are rarely suitable for direct publication. The PCA viewer's {\sl File} menu
includes a number of options for exporting the PCA matrix and transformed points
\includegraphics[width=2.5in]{images/trees1.pdf}
\includegraphics[width=2.5in]{images/trees2.pdf}
\includegraphics[width=1.25in]{images/trees4.pdf}
-\caption{{\bf Calculating Trees} Jalview provides four built in models for calculating trees. Jalview can also load precalculated trees in Newick format (right).}
+\caption{{\bf Calculating Trees} Jalview provides four built in models for calculating trees.
+Jalview can also load precalculated trees in Newick format (right).}
\label{trees1}
\end{center}
\end{figure}
\begin{figure}
\begin{center}
\includegraphics[width=5in]{images/trees3.pdf}
-\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate groups in Jalview}
+\caption{{\bf Interactive Trees} The tree level cutoff can be used to designate
+groups in Jalview.}
\label{trees2}
\end{center}
\end{figure}
% move to ch. 3 ?
%Both PCA and Tree viewers are linked analysis windows. This means that their selection and display are linked to a particular alignment, and control and reflect the selection state for a particular view.
-\subsubsection{Recovering input data for a tree or PCA plot calculation}
+\subsubsection{Recovering input Data for a Tree or PCA Plot Calculation}
\parbox[c]{5in}{
The {\sl File $\Rightarrow$ Input Data } option will open a new alignment window containing the original data used to calculate the tree or PCA plot (if available). This function is useful when a tree has been created and then the alignment subsequently changed.
}
\parbox[c]{1.25in}{\centerline{\includegraphics[width=1.25in]{images/pca_fmenu.pdf}
}}
-\subsubsection{Changing the associated view for a tree or PCA viewer}
+\subsubsection{Changing the associated View for a Tree or PCA Viewer}
\parbox[c]{4in}{
The {\sl View $\Rightarrow$ Associated Nodes With $\Rightarrow$ .. } submenu is shown when the viewer is associated with an alignment that is involved in multiple views. Selecting a different view does not affect the tree or PCA data, but will change the colouring and display of selected sequences in the display according to the colouring and selection state of the newly associated view.
} \parbox[c]{3in}{\centerline{
\exercise{Trees}{
-\exstep{Ensure that you have at least 1G memory available in Jalview (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}).}
+\exstep{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''.)}
\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, then 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.}
-\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 diferences 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.
+\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.
}
\exstep{Recover the {\sl Input Data} for the tree you just calculated from the {\sl File} menu. Check the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the alignment. Now select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}.
\exercise{Tree Based Conservation Analysis}{
\label{consanalyexerc}
\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
-\exstep{Build a Neighbourjoining tree using BLOSUM62 and use the {\sl Sort Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.}
-\exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
+\exstep{Build a Neighbour joining tree using BLOSUM62 and use the {\sl Sort
+Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.} \exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
-You may find it easier to browse the alignment if you first uncheck the {\sl View $\Rightarrow$ Show Annotations} option, and open the Overview Window to aid navigation.}
+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 to BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected)}
{\sl Note: You may want to save the alignment and tree as a project file, since
it is used in the next few exercises. } }
\caption{The Redundancy Removal dialog box opened from the edit menu. Sequences that exceed the current percentage identity threshold and are to be removed are highlighted in black.}
\end{figure}
-\exercise{Remove redundant sequences}{
+\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})}
-\exstep{Open the Remove Redundancy dialog and adjust the threshold to 90\%. Remove the sequences that are more than 90\% similar under this alignment.}
+tree based conservation analysis exercise (exercise \ref{consanalyexerc}). In
+the alignment window, you may need to deselect groups using Esc key.}
+\exstep{In the Edit menu select Remove Redundancy to open the Redundancy
+threshold selection dialog. Adjust the redundancy threshold value, start
+at 50 and increase the value to 65. Sequences selected will change colour in the Sequence ID panel. Select ``Remove'' to
+remove the sequences that are more than 65\% similar under this alignment.}
\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Mark Unlinked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
-\exstep{Use the [Undo] button on the dialog to recover the sequences. Note that the * symbols disappear from the tree display.}
+\exstep{Use the [Undo] button in the Redundancy threshold selection dialog box
+to recover the sequences. Note that the * symbols disappear from the tree display.}
\exstep{Experiment with the redundancy removal and observe the relationship between the percentage identity threshold and the pattern of unlinked nodes in the tree display.}
}
-\subsection{Subdividing the alignment according to specific mutations}
+\subsection{Subdividing the Alignment According to Specific Mutations}
It is often necessary to explore variations in an alignment that may correlate
with mutations observed in a particular region; for example, sites exhibiting
colourschemes can then be used to reveal any associated pattern of sequence
variation across the whole alignment.
-\subsection{Automated annotation of Alignments and Groups}
+\subsection{Automated Annotation of Alignments and Groups}
On loading a sequence alignment, Jalview will normally\footnote{Automatic
annotation can be turned off in the {\sl Visual } tab in the {\sl Tools
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
-Consensus} from the context menu. Quality is a measure of the inverse likelihood
-of unfavourable mutations in the alignment. Further details on these
+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.
-These annotations can be hidden and deleted but are only created on loading an
-alignment. If they are deleted then the alignment should be saved and reloaded
-to restore them. Jalview provides a toggle to autocalculate a consensus sequence
-upon editing. This is normally selected by default, but can be turned off for
+These annotations can be hidden and deleted via the context menu linked to the
+annotation row; but they are only created on loading an alignment. If they are
+deleted then the alignment should be saved and then reloaded to restore them.
+Jalview provides a toggle to autocalculate a consensus sequence upon editing. This is normally selected by default, but can be turned off for
large alignments {\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
Consensus} menu option if the interface is too slow.
Group associated consensus and conservation annotation rows reflect the
sequence variation within a particular group. Their calculation is enabled
by selecting the {\sl Group Conservation} or {\sl Group Consensus} options in
-the {\sl View $\Rightarrow$ Autocalculated Annotation } submenu of the alignment
-window.
+the {\sl Annotation $\Rightarrow$ Autocalculated Annotation } submenu of the
+alignment window.
\subsubsection{Alignment and Group Sequence Logos}
\label{seqlogos}
Sequence logos can be enabled by default for all new alignments {\sl via} the
Visual tab in the Jalview desktop's preferences dialog box.
-\exercise{Group conservation analysis}{
+\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{Create a new view, and ensure the annotation panel is displayed, and
-enable the display of {\sl Group Consensus} and the display of sequence
-logos to make it easier to see the different residue populations within each group.}
-\exstep{Select a column exhibiting about 50\% conservation that lies within the
-central conserved region of the alignment. Subdivide the alignment according to
+\exstep{In the View menu, create a new view. Ensure the annotation panel
+is displayed (Show annotation in 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. Then display of sequence
+logos to make it easier to see the different residue populations within each
+group. Activate logo by right clicking on the Consensus annotation row to open
+the pop-up 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. 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
defined. Click on the group annotation row IDs to select groups exhibiting a
a range of bioinformatics analysis tasks. }
\parbox[c]{1.75in}{\includegraphics[width=1.65in]{images/wsmenu.pdf}}
-\subsection{One-way web services}
+\subsection{One-Way Web Services}
-There are two types of one way service in jalview. Database services,
+There are two types of one way service in Jalview. Database services,
which were introduced in in Section \ref{fetchseq}, provide sequence and
alignment data. They can also be used to add sequence IDs to an alignment
imported from a local file, prior to further annotation retrieval, as described
\subsection{Remote Analysis Web Services}
Remote analysis services enable Jalview to use external computational
-facilities. There are curently three types of service - multiple sequence
+facilities. There are currently three types of service - multiple sequence
alignment, protein secondary structure prediction, and alignment analysis.
Many of these are provided by JABA servers, which are described at the end of
this section. In all cases, Jalview will construct a job based on the alignment
progress of running jobs.
-\subsection{JABA Web Services for sequence alignment and analysis}
+\subsection{JABA Web Services for Sequence Alignment and Analysis}
\label{jabaservices}
JABA stands for ``JAva Bioinformatics Analysis'', which is a system developed
by Peter Troshin and Geoff Barton at the University of Dundee for running
%%\item Learn how to install JABA services and configure Jalview to access them
%%\end{list}
-\subsection{Changing the Web Services menu layout}
+\subsection{Changing the Web Services Menu Layout}
\label{changewsmenulayout}
If you are working with a lot of different JABA services, you may wish to change
the way Jalview lays out the web services menu. You can do this from the Web
\exercise{Changing the Layout of the Web Services Menu}{
\label{changewsmenulayoutex}
\exstep{Make sure you have loaded an alignment into Jalview, and examine the
-current layout of the alignment windowÔøΩs {\sl Web Service} menu.}
+current layout of the alignment window's {\sl Web Service} menu.}
\exstep{Open the preferences dialog box and select the web services tab.}
\exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
the {\sl Enable Enfin Services} checkboxes.}
Test results from JABAWS are reported on Jalview's console output (opened from
the Tools menu). Tests are re-run every time Jalview starts, and when the
-[Refresh] button is pressed on the Jalview JABAWS configuration panel.
+[Refresh Services] button is pressed on the Jalview JABAWS configuration panel.
-\subsubsection{Resetting the JABA services setting to their defaults}
+\subsubsection{Resetting the JABA Services Setting to their Defaults}
Once you have configured a JABAWS server and selected the OK button of the
preferences menu, the settings will be stored in your Jalview preferences file,
along with any preferences regarding the layout of the web services menu. If
you should ever need to reset the JABAWS server list to its defaults, use the
`Reset Services' button on the Web Services preferences panel.
-\subsection{Running your own JABA server}
+\subsection{Running your own JABA Server}
You can download and run JABA on your own machine using the `VMWare' or
VirtualBox virtual machine environments. If you would like to learn how to do
this, there are full instructions at the
\href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}.
-\exercise{Installing a JABA Virtual Machine on your computer}{
+\exercise{Installing a JABA Virtual Machine on your Computer}{
\label{jabawsvmex}{\sl This tutorial will demonstrate the simplest way of
installing JABA on your computer, and configuring Jalview so it can access the JABA services.
this will begin with `http:' and end with `/jabaws''.}
}
-\exercise{Configuring Jalview to access your new JABAWS virtual appliance}{
+\exercise{Configuring Jalview to Access your new JABAWS Virtual Appliance}{
\label{confnewjabawsappl}
\exstep{Start Jalview (If you have not done so already).}
\exstep{Enable the Jalview Java Console by selecting its option from the Tools
T-COFFEE is the slowest, but also the most accurate. ClustalW is historically
the most widely used. Muscle is faster than ClustalW and probably the most
accurate for smaller alignments and MAFFT is probably the best for large
-alignments, however Clustal Omega, which was released in 2011, is arguably the
-fastest and most accurate tool for protein multiple alignment.
+alignments, however {\bf Clustal Omega}, which was released in 2011, is
+arguably the fastest and most accurate tool for protein multiple alignment.
To run an alignment web service, select the appropriate method from the {\sl
\parbox[c]{2in}{\includegraphics[width=2in]{images/ws3.pdf}}
\caption{{\bf Multiple alignment via web services} The appropriate method is
selected from the menu (left), a status box appears (centre), and the results
-appear in a new window (right)}
+appear in a new window (right).}
\label{webservices}
\end{center}
\end{figure}
Omega. When performing a re-alignment, Jalview submits the current selection to
the alignment service complete with any existing gaps. This approach is useful
when one wishes to align additional sequences to an existing alignment without
-any further optimisation to the existing alignment. The Re-alignment service
+any further optimisation to the existing alignment. The re-alignment service
provided by ClustalW in this case is effectively a simple form of profile
alignment.
-\subsubsection{Alignments of sequences that include hidden regions}
+\subsubsection{Alignments of Sequences that include Hidden Regions}
If the view or selected region that is submitted for alignment contains hidden
regions, then {\bf only the visible sequences will be submitted to the service}.
in the input data prior to their display in a new window. This approach ensures
that 1) hidden column boundaries in the input data are preserved in the
resulting alignment - in a similar fashion to the constraint that hidden columns
-place on alignment editing (see Section \ref{lockededits}), and 2) hidden
+place on alignment editing (see Section \ref{lockededits} and 2) hidden
columns can be used to preserve existing parts of an alignment whilst the
visible parts are locally refined.
\exercise{Multiple Sequence Alignment}{
\exstep{ Close all windows and open the alignment at {\sf
http://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 first sequence set by clicking on the window and try running ClustalW and 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 them and then submit the view for re-alignment with ClustalW.}
-\exstep{Use [CTRL]-Z to recover the alignment of the last three sequences in the MAFFT alignment. Once the ClustalW 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. Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults} to submit the visible portion of the alignment to MAFFT. When the web service job pane appears, note that there are now two alignment job status panes shown in the window.}
-\exstep{When the MAFFT job has finished, compare the alignment of the N-terminal visible region in the result with the corresponding region of the original alignment. If you wish, select and hide a few more columns in the N-terminal region, and submit the alignment to the service again and explore the effect of local alignment on the non-homologous parts of the N-terminal region.}
-}
-
-
-\subsection{Customising the parameters used for alignment}
+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{Return to the first sequence alignment window by clicking on
+ the window, and repeat using Clustal and 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 them and then
+submit the view for re-alignment with Clustal.}
+\exstep{Use [CTRL]-Z to recover the alignment of the last three sequences in the MAFFT alignment.
+Once the Clustal 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.
+Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults} to
+submit the visible portion of the alignment to MAFFT. When the web service job pane appears,
+note that there are now two alignment job status panes shown in the window.}
+\exstep{When the MAFFT job has finished, compare the alignment of the N-terminal visible
+region in the result with the corresponding region of the original alignment. If you wish,
+select and hide a few more columns in the N-terminal region, and submit the alignment to the
+service again and explore the effect of local alignment on the non-homologous parts of the
+N-terminal region.}
+}
+
+
+\subsection{Customising the Parameters used for Alignment}
JABA web services allow you to vary the parameters used when performing a
bioinformatics analysis. For JABA alignment services, this means you are
\end{list}
-\subsubsection{Getting help on the parameters for a service}
+\subsubsection{Getting Help on the Parameters for a Service}
Each parameter available for a method usually has a short description, which
-jalview will display as a tooltip, or as a text pane that can be opened under
+Jalview will display as a tooltip, or as a text pane that can be opened under
the parameter's controls. In the parameter shown in Figure
\ref{clustalwparamdetail}, the description was opened by selecting the button on the left hand side. Online help for the
service can also be accessed, by right clicking the button and selecting a URL
pre-defined sets of parameters suited for particular types of alignment
problem. For instance, the Muscle service provides the following presets:
\begin{list}{$\bullet$}{}
-\item Huge
+\item Large alignments (balanced)
\item Protein alignments (fastest speed)
\item Nucleotide alignments (fastest speed)
\end{list}
The presets are displayed in the JABA web services submenu, and can also be
accessed from the parameter editing dialog box, which is opened by selecting
-the `{\sl Edit settings and run ...}' option from the web serviceÔøΩs menu. If you have used
+the `{\sl Edit settings and run ...}' option from the web services menu. If you have used
a preset, then it will be mentioned at the beginning of the job status file shown
in the web service job progress window.
can handle, then an error message will be shown informing you of the maximum
number allowed by the server.
-\subsection{User defined Presets}
+\subsection{User Defined Presets}
Jalview allows you to create your own presets for a particular service. To do
this, select the `{\sl Edit settings and run ...}' option for your service,
which will open a parameter editing dialog box like the one shown in Figure
\label{jwsparamsdialog} }
\end{figure}
-\subsubsection{Saving parameter sets}
+\subsubsection{Saving Parameter Sets}
When creating a custom parameter set, you will be asked for a file name to save
it. The location of the file is recorded in the Jalview user preferences in the
same way as a custom alignment colourscheme, so when Jalview is launched again,
% }
% }
-\section{Protein alignment conservation analysis}
+\section{Protein Alignment Conservation Analysis}
\label{aacons}
The {\sl Web Service $\Rightarrow$ Conservation} menu controls the computation
of up to 17 different amino acid conservation measures for the current alignment
score developed by Manning et al. in 2008.\footnote{SMERFS Score Manning et al. {\sl BMC
Bioinformatics} 2008, {\bf 9} 51 \href{http://dx.doi.org/10.1186/1471-2105-9-51}{doi:10.1186/1471-2105-9-51}}
-\subsubsection{Enabling and disabling AACon calculations}
+\subsubsection{Enabling and Disabling AACon Calculations}
When the AACon Calculation entry in the {\sl Web Services $\Rightarrow$
Conservation} menu is ticked, AACon calculations will be performed every time
the alignment is modified. Selecting the menu item will enable or disable
automatic recalculation.
-\subsubsection{Configuring which AACon calculations are performed}
+\subsubsection{Configuring which AACon Calculations are Performed}
The {\sl Web Services $\Rightarrow$ Conservation $\Rightarrow$ Change AACon
Settings ...} menu entry will open a web services parameter dialog for the
currently configured AACon server. Standard presets are provided for quick and
AACon settings for an alignment are saved in Jalview projects along with the
latest calculation results.
-\subsubsection{Changing the server used for AACon calculations}
+\subsubsection{Changing the Server used for AACon Calculations}
If you are working with alignments too large to analyse with the public JABAWS
server, then you will most likely have already configured additional JABAWS
servers. By default, Jalview will chose the first AACon service available from
\label{protdisorderpred}
Disordered regions in proteins were classically thought to correspond to
-'linkers' between distinct protein domains, but disorder can also play a role in
+``linkers'' between distinct protein domains, but disorder can also play a role in
function. The {\sl Web Services $\Rightarrow$ Disorder} menu in the alignment window
allows access to protein disorder prediction services provided by the configured
JABAWS servers.
-\subsection{Disorder prediction results}
+\subsection{Disorder Prediction Results}
Each service operates on sequences in the alignment to identify regions likely
to be unstructured or flexible, or alternately, fold to form globular domains.
As a consequence, disorder predictor results include both sequence features and
\end{center}
\end{figure}
-\subsubsection{Navigating large sets of disorder predictions}
+\subsubsection{Navigating Large Sets of Disorder Predictions}
{\bf Figure \ref{alignmentdisorderannot}} shows a single sequence annotated with
a range of disorder predictions. Disorder prediction annotation rows are
\end{figure}
-\subsection{Disorder predictors provided by JABAWS 2.0}
+\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
\label{protdispredex}
\exstep{Open the alignment at
-\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
+\url{http://www.jalview.org/tutorial/interleukin7.fa}. } also available at
-\exstep{Run the DISEMBL disorder predictor {\slvia} the {\slWeb Services
+
+\url{http://www.jalview.org/tutorial/training-materials/2014/Dundee/Oct/interleukin7.fa}
+
+\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Services
$\Rightarrow$ Disorder Prediction } submenu.}
\exstep{Use {\sl Sequence ID $\Rightarrow$ Structure $\Rightarrow$ Discover PDB
sequence features, whilst webservices like JNet (see \ref{jpred} above) can be used to analyse a given sequence or alignment and generate annotation for it.
-\subsection{Creating sequence features}
+\subsection{Creating Sequence Features}
Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialogue box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.
\begin{figure}[htbp]
\end{center}
\end{figure}
-Creation of features from a selection spanning multiple sequences results in the creation of one feature per sequence. Each feature remains associated with it's own sequence.
+Creation of features from a selection spanning multiple sequences results in the creation of one feature per sequence.
+Each feature remains associated with its own sequence.
-\subsection{Customising feature display}
+\subsection{Customising Feature Display}
Feature display can be toggled on or off by selecting the {\sl View
$\Rightarrow$ Show Sequence Features} menu option. When multiple features are
Features file format for the import of sequence annotation. Features and
alignment annotation are also extracted from other formats such as Stockholm,
and AMSA. URL links may also be attached to features. See the online
-documentation for more details of the additional capabilities of the jalview
+documentation for more details of the additional capabilities of the Jalview
features file.
-\exercise{Creating features}{
-\exstep{Open the alignment at \textsf{http://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 to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}. A dialogue box will appear.
+\exercise{Creating Features}{
+\exstep{Open the alignment at \textsf{http://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
+to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}.
+A dialogue box will appear.
}
\exstep{
Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
now displayed. Close the sequence feature settings box by clicking OK or
Cancel.} }
-\subsection{Creating user defined annotation}
+\subsection{Creating User Defined Annotation}
Annotations are properties that apply to the alignment as a whole and are visualized on rows in the annotation panel.
To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}). A dialogue box appears. Enter the label to use for this row and a new row will appear.
\end{center}
\end{figure}
-\exercise{Annotating alignments}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Right-click on the annotation label for {\sl Conservation} 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.
+\exercise{Annotating Alignments}{
+\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.
}
\exstep{
-Navigate to column 97. Select column 97 on the new annotation row. Right click on the 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}. Choose a colour from the colour chooser dialogue and click 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 sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet arrow.
-}
-\exstep{Right click on the 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 the [To Textbox] button.
-
-The format for this file is given in the Jalview help. Press [F1] to open it, and find the ``Annotations File Format'' entry in the ``Alignment Annotations'' section of the contents pane. }
-
-\exstep{Export the file to a text editor and edit the file to change the name of the annotation 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 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} 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 row entry in the file, and create an annotation row grouping to overlay the three quantitative annotation rows.}
+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}.
+Choose a colour from the colour chooser dialogue
+and click 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
+ sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet
+ 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
+the [To Textbox] button.
+
+The format for this file is given in the Jalview help. Press [F1] to open it, and find
+the ``Annotations File Format'' entry in the ``Alignment Annotations'' section of the contents
+pane. }
+
+\exstep{Export the file to a text editor and edit the file to change the name of the annotation
+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
+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}
+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
+row entry in the file, and create an annotation row grouping to overlay the three quantitative
+annotation rows.}
}
\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 annotation. } }
+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
+annotation. } }
-\section{Importing features from databases}
+\section{Importing Features from Databases}
\label{featuresfromdb}
Jalview supports feature retrieval from public databases either directly or {\sl
via} the Distributed Annotation System (DAS\footnote{http://www.biodas.org/}).
do not match the coordinate system from which the features were defined, then
the features will be displayed incorrectly.
-\subsubsection{Viewing and exporting a sequence's database annotation}
+\subsubsection{Viewing and Exporting a Sequence's Database Annotation}
You can export all the database cross references and annotation terms shown in
the sequence ID tooltip for a sequence by right-clicking and selecting the {\sl
\parbox[c]{3in}{
\centerline{\includegraphics[width=2.2in]{images/seqdetailsreport.pdf}}}
-\subsubsection{Automatically discovering a sequence's database references}
+\subsubsection{Automatically Discovering a Sequence's Database References}
Jalview includes a function to automatically verify and update each sequence's
start and end numbering against any of the sequence databases that the {\sl
Sequence Fetcher} has access to. This function is accessed from the {\sl
\exstep{Load the example alignment at http://www.jalview.org/tutorial/alignment.fa}
\exstep{Verify that there are no database references for the sequences by first
checking that the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ Show
-Database IDs} option is selected, and then mousing over each sequence's ID.}
+Database Refs} option is selected, and then mousing over each sequence's ID.}
\exstep{Use the {\sl Webservice $\Rightarrow$ Fetch DB References} menu option to retrieve database IDs for the sequences.}
\exstep{Examine the tooltips for each sequence in the alignment as the retrieval progresses - note the appearance of new database references.}
\exstep{Once the process has finished, save the alignment as a Jalview Project.}
by checking the labelled box at the top of the panel.
-\subsubsection{The Fetch Uniprot IDs dialog box}
+\subsubsection{The Fetch Uniprot IDs Dialog Box}
\label{discoveruniprotids}
If any sources are selected which refer to Uniprot coordinates as their reference system, then you may be asked if you wish to retrieve Uniprot IDs for your sequence. Pressing OK instructs Jalview to verify the sequences against Uniprot records retrieved using the sequence's ID string. This operates in much the same way as the {\sl Web Service $\Rightarrow$ Fetch Database References } function described in Section \ref{fetchdbrefs}. If a sequence is verified, then the start/end numbering will be adjusted to match the Uniprot record to ensure that features retrieved from the DAS source are rendered at the correct position.
-\subsubsection{Rate of feature retrieval}
+\subsubsection{Rate of Feature Retrieval}
Feature retrieval can take some time if a large number of sources is selected and if the alignment contains a large number of sequences. This is because Jalview only queries a particular DAS source with one sequence at a time, to avoid overloading it. As features are retrieved, they are immediately added to the current alignment view. The retrieved features are shown on the sequence and can be customised as described previously.
-\exercise{Retrieving features with DAS}{
+\exercise{Retrieving Features with DAS}{
\label{dasfeatretrexcercise}
\exstep{Load the alignment at
\textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl View
$\Rightarrow$ Feature Settings \ldots} from the alignment window menu. Select
-the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netnglyc. Click OK. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment. } \exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Sequence Feature Settings window. }
-\exstep{Move the mouse over the sequence ID panel. Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
-\exstep{Search through the alignment to find a feature with a link symbol next to it. Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
+the {\sl DAS Settings} tab. A long list of available DAS sources is listed.
+Select a small number, eg Uniprot, DSSP, signalP and netnglyc. Click.
+A window may prompt whether you wish Jalview to fetch DAS features. Click {\sl
+Yes}.
+Jalview will start retrieving features. As features become available they will be mapped onto the alignment. }
+\exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button.
+Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip.
+Close the Sequence Feature Settings window. }
+\exstep{Move the mouse over the sequence ID panel.
+Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
+\exstep{Search through the alignment to find a feature with a link symbol next to it.
+Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
% TODO this doesn't work ! \includegraphics[width=.3in]{images/link.pdf}
\exstep{
}
}
-\subsection{Colouring features by score or description
-text}
+\subsection{Colouring Features by Score or Description
+Text}
\label{featureschemes}
Sometimes, you may need to visualize the differences in information carried by
sequence features of the same type. This is most often the case when features
style and a greater than ($>$) or less than ($<$) symbol to indicate when a
threshold has been defined.
-\subsection{Using features to re-order the alignment}
+\subsection{Using Features to Re-order the Alignment}
\label{featureordering}
The presence of sequence features on certain sequences or in a particular
region of an alignment can quantitatively identify important trends in
then only features found in that region of the alignment will be used to
create the new alignment ordering.
-% \exercise{Shading and sorting alignments using sequence features}{
+% \exercise{Shading and Sorting Alignments using Sequence Features}{
% \label{shadingorderingfeatsex}
%
% This exercise is currently not included in the tutorial because no DAS servers
Jalview has limited knowledge of the capabilities of the programs that
are made available to it {\sl via} web services, so it is up to you, the user,
to decide which service to use when working with nucleic acid sequences. The
-table below shows which alignment programs are most appropriate
+table shows which alignment programs are most appropriate
for nucleotide alignment. Generally, all will work, but some may be more suited
to your purposes than others. We also note that none of these include
support for taking RNA secondary structure prediction into account when aligning
-sequences (but will be providing services for this in the future!).
+sequences (but will be providing services for this in the future!)
\begin{table}{}
\centering
\begin{tabular}{|l|c|l|}
}
-\subsection{Coding regions from EMBL records}
+\subsection{Coding Regions from EMBL Records}
Many EMBL records that can be retrieved with the sequence fetcher contain exons.
Coding regions will be marked as features on the EMBL nucleotide sequence, and
\subsubsection{Retrieval of Protein or DNA Cross References}
The {\sl Calculate $\Rightarrow$ Get Cross References } function is only available when Jalview recognises that there are protein/DNA cross-references present on sequences in the alignment. When selected, it retrieves the cross references from the alignment's dataset (a set of sequence and annotation metadata shared between alignments) or using the sequence database fetcher. This function can be used for EMBL sequences containing coding regions to open the Uniprot protein products in a new alignment window. The new alignment window that is opened to show the protein products will also allow dynamic highlighting of codon positions in the EMBL record for each residue in the protein product(s).
-\subsubsection{Retrieval of protein DAS features on coding regions}
+\subsubsection{Retrieval of Protein DAS Features on Coding Regions}
The Uniprot cross-references derived from EMBL records can be used by Jalview to visualize protein sequence features directly on nucleotide alignments. This is because the database cross references include the sequence coordinate mapping information to correspond regions on the protein sequence with that of the nucleotide contig. Jalview will use the Uniprot accession numbers associated with the sequence to retrieve features, and then map them onto the nucleotide sequence's coordinate system using the coding region location.
\end{center}
\end{figure}
-\exercise{Visualizing protein features on coding regions}
+\exercise{Visualizing Protein Features on Coding Regions}
{
\exstep{Use the sequence fetcher to retrieve EMBL record D49489.}
-\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the alignment view format to Wrapped mode so the distinct exons can be seen.}
-\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots} window and fetch features for D49489 from the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
+\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the
+alignment view format to Wrapped mode so the distinct exons can be seen.}
+\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots}
+window {\sl View $\Rightarrow$ Features setting}
+and fetch features for D49489 from the Uniprot reference server,
+and any additional servers that work with the Uniprot coordinate system.}
\exstep{Mouse over the features retrieved, note that they have been mapped onto the coding regions, and in some cases broken into several parts to cover the distinct exons.}
\exstep{Open a new alignment view containing the Uniprot protein product with {\sl Calculate $\Rightarrow$ Get Cross References $\Rightarrow$ Uniprot } and examine the database references and sequence features. Experiment with the interactive highlighting of codon position for each residue.
}
It also allows the extraction of RNA secondary structure from 3D data when
available.
-\subsection{Performing RNA secondary structure predictions}
+\subsection{Performing RNA Secondary Structure Predictions}
Secondary structure consensus calculations can be performed by enabling the
VIENNA service {\sl via} the {\sl Web Services $\Rightarrow$ Secondary
Structure} menu. These consensus structures are created by analysing the
\end{figure}
-\exercise{Viewing RNA structures}{
-\label{viewingrnaex}
+\exercise{Viewing RNA Structures}
+{ \label{viewingrnaex}
-\exstep{Import RF00162 from Rfam (Full).}
+\exstep{Import RF00162 from Rfam (Full) using Fetch sequence(s) option in File
+menu.}
\exstep{Select {\sl Colour by RNA Helices} to shade the alignment by
the secondary structure annotation provided by Rfam.}
+
\exstep{Open VARNA with {\sl Structure $\Rightarrow$ View Structure
$\Rightarrow$ RNA Secondary Structure}.
+In the VARNA Structures Manager toggle between (i) secondary structure
+(alignment) (with gaps) and (ii) trimmed secondary structure (alignment).
+Explore the difference between trimmed and untrimmed views.
+Click on different residues and located them in the sequence alignment window.}
- Explore the difference between trimmed and untrimmed views for the
- structure.
-}
-\exstep{Add and link a Jmol structure view
-for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
-structure along-side the consensus structure for the alignment by adding
-reference annotation from the 3D structure.
-
-{\sl Hint: You need to make sure the RNAview service is enabled in your {\sl
-Structure} preferences to obtain RNA secondary structure annotation from PDB
-files.}}
+\exstep{In the VARNA Structures Manager, right click on display window to
+bring up the pop up context menu. Investigate option within File, Export, Display
+and Edit sections.}
-\exstep{Perform a secondary structure prediction. Enable the VIENNA consensus
-calculation via the {\sl Web Services} menu. Compare this with the annotation
-line provided by Rfam.}
+\exstep{Perform a secondary structure prediction in {\sl Web Services}. Enable
+the VIENNA consensus calculation via the {\sl Web Services} menu and select
+Change RNAAIiFold settings option.}
+% Compare this with the annotationline provided by Rfam.
\exstep{Edit the VIENNA calculation settings to show
-Base Pair probabilities.
+Base Pair probabilities. Explore how editing the alignment affects the consensus
+calculation.}
+
+\exstep{Import 2GIS from PDB database using Fetch sequence(s) option.}
+\exstep{Click on a sequence in Sequence ID panel and select {\sl Structure
+$\Rightarrow$ View Structure $\Rightarrow$ 2GIS}, to view the structure in Jmol
+window. Click on different residues and located them in the sequence alignment window.}
+%\exstep{Add and link a Jmol structure view
+%for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
+%structure along-side the consensus structure for the alignment by adding
+%reference annotation from the 3D structure.
+
+%{\sl Hint: You need to make sure the RNAview service is enabled in your {\sl
+%Structure} preferences to obtain RNA secondary structure annotation from PDB
+%files.}}
-Explore how editing the alignment affects the consensus
-calculation.} }
+ }
\end{document}
git://source.jalview.org / jalview-manual.git / blobdiff