School of Life Sciences, University of Dundee
Dundee, Scotland DD1 5EH, UK
-
\vspace{2in}
-Manual Version 1.9
-
-Manual Version 1.8.1
+Manual Version 1.9.1
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-10th November 2017
+10th November 2017
\end{center}
\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
close all windows.}
\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.
-
+Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{http://www.jalview.org/tutorial/alignment.fa} in the box.
Click {\sl OK} to load the alignment.}
+
\exstep{{\bf Loading sequences from a file:} Close all windows using the
-{\sl Window $\Rightarrow$ Close All} menu option from the Desktop.
+{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser and save the file to your desktop.
+your web browser and save the file to your desktop using {\sl File
+$\Rightarrow$ Save Page as}.
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 {\sl OK} to load.}
-\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
-
-(i) Select {\sl Desktop $\Rightarrow$ Window
-$\Rightarrow$ Close All}. Then drag the alignment.fa file from the desktop and
-drop it onto the Jalview window, the alignment should open.
+$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
+Select the file and click {\sl OK} to load.}
-(ii) Test the differences
-between (a) dragging the sequence onto the Jalview desktop and (b)
-dragging the sequence onto an existing alignment window.
-
-(iii) Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
-web browser. Drag the URL directly from browser onto Jalview desktop. (If
-the URL is downloaded, then locate the file in your
-download directory and open it in a text editor.)}
+\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
+(i) Drag the alignment.fa file that you have just saved from its folder and
+drop it onto the Jalview desktop window, the alignment should open.
+
+(ii) Open
+\url{http://www.jalview.org/examples/estrogenReceptorProtein.fa} in a web
+browser. Test the differences
+between (a) dragging the URL directly from browser onto the Jalview
+desktop.
+(If the URL is downloaded, alternatively locate the file in your download
+directory and drag it onto the desktop.) (b) dragging the URL from
+browser onto the existing alignment.fa alignment window in the Jalview desktop.
+
+(iii) Open \url{http://www.jalview.org/examples/estrogenReceptorCdna.fa} in a web
+browser. Note that this is a cDNA file. Drag the URL from
+browser onto the estrogenReceptorProtein.fa protein alignment window in
+the Jalview desktop. A dialogue box opens asking `Would you like to open as split
+window, with cDNA and protein linked?' select `Split Window' option. A
+split window opens in the Jalview desktop.
+}
\exstep{{\bf The text editor:} (i) Open the alignment.fa file using text editor.
-Copy the sequence text from the file into the clipboard and paste it into the desktop
-background by right-clicking and selecting the {\sl Paste to New Window} menu
-option.
+Copy the sequence text into the clipboard using [CTRL]-A and then [CTRL]-C.
-(ii) In the text editor, copy the sequence text from
-alignment.fa into the clipboard (usually {\sl via} the browser's {\sl Edit
-$\Rightarrow$ Copy} menu option).
+(ii) Place the mouse on the Jalview desktop and right-click the mouse
+to open the context window. Select the {\sl Paste to New Window} menu option.
-(iii) In the Desktop menu, select {\sl File
+(iii) In the Jalview desktop menu, select {\sl File
$\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox}.
-Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$
-Paste} text box menu option. Click {\sl New Window} and the alignment will be
-loaded.}
+Paste the clipboard into the large window using [CTRL]-V. Click {\sl New Window}
+and the alignment will be loaded.}
\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
-$\Rightarrow$ Fetch Sequence(s)...} from the Desktop. The {\sl Select Database
-Retrieval Source} dialog will open showing all the database sources. Select the
-{\bf PFAM seed} database and click {\sl OK}.
+$\Rightarrow$ Fetch Sequence(s)...} from the Jalview desktop menu. The {\sl
+Select Database Retrieval Source} dialog will open listing all the database
+sources. Select the {\bf PFAM seed} database and click {\sl OK}.
-(ii)Once a source has been selected, the {\sl New
+(ii) The {\sl New
Sequence Fetcher} window will open. Enter the accession number {\bf PF03460}
and click {\sl OK}.
An alignment of about 174 sequences should load.}
\exstep{These can be viewed using the Overview window accessible from {\sl View
-$\Rightarrow$ Overview Window.}
-Several database IDs can be loaded by using semicolons to separate them.}
+$\Rightarrow$ Overview Window.}}
{\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}} }
suitable folder.}
\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. }
+$\Rightarrow$ Load Project} menu option. Observe how many of the windows are as they were when they were saved. }
{\bf See the video at: \url{http://www.jalview.org/Help/Getting-Started}.}
}
\exercise{Making Selections and Groups}{
\label{exselect}
-\exstep{Close windows.
-
-Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
+\exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
}
\exstep{Selecting an arbitrary region. Choose a residue and place the mouse
cursor on it (residue information will show in alignment window status
sequence group.
\exercise{Hiding and Revealing Regions}{
-\exstep{Close windows.
-
-Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
+\exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
}
\exstep{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
\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.
+Clustal} 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)
\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 this icon up or down.}
-}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\subsection{Graphical Output}
\label{figuregen}
Photoshop, Illustrator, Inkscape, Ghostview, Powerpoint (Windows), or
Preview (Mac OS X). Zoom in and note that the image has near-infinite
resolution.}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.
}
% left out for Glasgow 2016
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.
+\exstep{Right click on the title text in the annotation row that you just
+created.
Select {\sl Export Annotation} in context menu and, in the Export Annotation
dialog box that will open, select the Jalview format and click the {\sl [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. }
+(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.}
Note the
SEQUENCE\_REF statements surrounding the row specifying the sequence association for the
annotation.
-}}
+}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\section{Importing Features from Databases}
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.
+Roll the mouse over the features and you will see that the feature has moved
+with the sequence. Delete the gap you created using {\sl Edit
+$\Rightarrow$ Undo}.
}
\exstep{
Add a similar feature to column 102. When the feature dialog box appears, clicking the Sequence Feature
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 {\sl OK} or
-{\sl Cancel}.} }
+{\sl Cancel}.}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\chapter{Multiple Sequence Alignment}
\label{msaservices}
to the existing alignment. ClustalO's realignment works by generating a
probabilistic model (a.k.a HMM) from the original alignment, and then realigns
{\bf all} sequences to this profile. For a well aligned MSA, this process
-will simply reconstruct the original alignment (with additonal sequences), but
+will simply reconstruct the original alignment (with additional sequences), but
in the case of low quality MSAs, some differences may be introduced.
\begin{figure}[htbp]
\exercise{Principal Component Analysis}
{ \exstep{Load the alignment at
\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
-\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principal Component
-Analysis}.
-A new window will open. Move this window within the desktop so that the tree,
-alignment and PCA viewer windows are all visible.
+\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window and a dialogue box will open. Select the Principal Component Analysis option
+and then click the Calculate button.}
+\exstep{Move
+this window within the desktop so that the alignment and PCA viewer windows are 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 the sequences on the
alignment.
-} \exstep{ Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
-Neighbour Joining Using BLOSUM62}. A new tree window will appear.
-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.
+} \exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window. In dialogue box select Neighbour
+Joining and in the drop-down list select BLOSUM62. Click the Calculate button
+and a tree window will open.}
+\exstep{Place the mouse cursor on the tree so that the
+tree partition divides the tree into a number of groups, each with a
+different (arbitrarily selected) 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.}
{\bf See the video at:
- unmatched leaves will still be displayed, and can be highlighted using the
{\sl View $\Rightarrow$ Mark Unlinked Leaves} menu option.
+\exercise{Trees}
+{{\sl Ensure that you have at least 1G memory available in Jalview.
+(Start with 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 table in the Development section of the Jalview web site
+(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds}), go
+to ``latest official build'' row and in the ``Webstart'' column, click
+on ``2G''.)}
+
+\exstep{Open the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa}.}
+
+\exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window and a dialogue box opens. In the tree section select Neighbour
+Joining, in the drop-down list select BLOSUM62 and click the Calculate
+button. A tree window will open.}
+
+\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 tree window, select {\sl View $\Rightarrow$ Sort Alignment
+by Tree}. The sequences are reordered to match the order in the tree and groups
+ are formed implicitly. Alternatively in the alignment window, select
+{\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$
+ Neighbour Joining Tree using BLOSUM62 from...}.}
+
+\exstep{Select {\sl Calculate $\Rightarrow$ Tree or PCA..}. in the alignment
+window. In the dialogue box, select Average Distance and in the drop down
+list select BLOSUM62. Click the Calculate button and a new
+tree window will appear. The group colouring makes it easy to see the differences between the two
+trees calculated by the different methods.}
+
+\exstep{In the alignment window, select sequence 2 from
+column 60 to sequence 12 and column 123. Select {\sl Calculate $\Rightarrow$
+Tree or PCA..}. , in the dialogue box select Neighbour Joining and
+BLOSUM62, then click the Calculate button.
+ A tree will appear containing 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.
+
+{\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+
+}
\begin{figure}
\begin{center}
Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
can help when working with larger alignments.
-\exercise{Trees}
-{Ensure that you have at least 1G memory available in Jalview.
-{\sl (Start with 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 table, go to ``latest official build'' row and ``Webstart'' column, click
-on ``2G''.)}
-\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 tree window opens.}
-\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 by the 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. 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 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 $\Rightarrow$
+%Neighbour Joining Using BLOSUM62}.
-{\bf See the video at:
-\url{http://www.jalview.org/training/Training-Videos}.}
-}
+%A warning dialog box {\bf ``Sequences not aligned'' } appears because the
+% sequences input to the tree calculation are of different lengths. }
-\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 $\Rightarrow$
-Neighbour Joining Using BLOSUM62}.
+%\exstep{Select {\sl Edit $\Rightarrow$ tick Pad Gaps } and perform the
+%tree calculation again. This time a new tree should appear - because padding
+%gaps ensures all the sequences are the same length after editing.}
+%{\sl Pad Gaps } option
+%can be set in Preferences using
+%{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
-A warning dialog box {\bf ``Sequences not aligned'' } appears because the sequences input to the tree calculation are of different lengths. }
+%{\bf See the video at:
+%\url{http://www.jalview.org/training/Training-Videos}.}
+%}
-\exstep{Select {\sl Edit $\Rightarrow$ tick Pad Gaps } and perform the
-tree calculation again. This time a new tree should appear - because padding
-gaps ensures all the sequences are the same length after editing.}
-{\sl Pad Gaps } option
-can be set in Preferences using
-{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
+ \exercise{Tree Based Conservation Analysis}{
+\label{consanalyexerc}
+\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher.
+Select {\sl Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation}, set
+ {\sl Conservation} shading threshold at around 20. }
+ \exstep{Build a Neighbour joining tree by selecting {\sl Calculate
+ $\Rightarrow$ Tree or PCA..}. in the alignment window. In the dialogue box, select Neighbour
+Joining and in the drop-down
+list select BLOSUM62, then click the Calculate button.}
+\exstep{Use the cursor to select a point on the tree to partition the
+alignment into groups.}
+\exstep {Select {\sl View $\Rightarrow$ Sort Alignment By Tree} option in the
+tree window to re-order the sequences in the alignment.
+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. Open the
+Overview Window from the View menu to aid navigation.}
+
+\exstep{Try changing the colourscheme of the residues in the alignment 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 set of exercises. }
{\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
}
-% \exercise{Tree Based Conservation Analysis}{
-%\label{consanalyexerc}
-%\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher.
-%Select {\sl Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation}, set
-% {\sl Conservation} shading threshold at around 20. } \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 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. Open the
-%Overview Window within the View menu to aid navigation.}
-
-%\exstep{Try changing the colourscheme of the residues in the alignment 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 set of exercises. }
-
-%{\bf See the video at:
-%\url{http://www.jalview.org/training/Training-Videos}.}
-%}
-
\subsection{Redundancy Removal}
retrieval (See \ref{fetchdbrefs}) to discover identifiers for the
sequences to use to search the PDB. This can take a
few seconds for each sequence and will be performed for all selected
-sequences.\footnote{After this is done, you can can see the added database
+sequences.\footnote{After this is done, you can see the added database
references in a tool tip by mousing over the sequence ID. You can use the {\sl
View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ Show Db References }
submenu option to enable or disable these data in the tooltip.}
\exstep{Repeat the previous two steps for each of the other
alignments. In each case, after selecting the DNMT1\_MOUSE.pdb structure and
hitting the `View' button on the Structure Chooser dialog, Jalview will ask if you wish to create
-a new Jmol view. Respond {\bf `Yes'} each time. This will ensure ensure each sequence
+a new Jmol view. Respond {\bf `Yes'} each time. This will ensure each sequence
fragment is associated with the {\bf same} Jmol view. }
\exstep{Pick a different
Ensure that you first disable the {\sl View $\Rightarrow$ Show Features} menu
option, or you may not see any colour changes in the associated structure.
-{\sl Examine the regions strongly coloured at the interfaces betweeen each
+{\sl Examine the regions strongly coloured at the interfaces between each
protein domain, and the DNA binding region. What do you think these patterns
mean ? } }
\exstep{Save your work as a Jalview project and verify that it can be opened
prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
\end{list}
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2.25in]{images/jpred1.pdf}
-\includegraphics[width=3in]{images/jpred2.pdf}
-\caption{{\bf Secondary Structure Prediction} Status (left) and results (right)
-windows for JPred predictions. }
-\label{jpred}
-\end{center}
-\end{figure}
-
-
-Jpred is launched in the same way as the other web services. Select {\sl Web
-Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JPred
-Secondary Structure Prediction}\footnote{JNet is the Neural Network based
-secondary structure prediction method that the JPred server uses.} from the
-alignment window menu (Figure \ref{jpred}).
-A status window opens to inform you of the progress of the job. Upon completion, a new alignment window opens and the Jpred
-predictions are included as annotations. Consult the Jpred documentation for
-information on interpreting these results.
-
-\subsection{Hidden Columns and JPred Predictions}
-\label{hcoljnet}
-Hidden columns can be used to exclude parts of a sequence or profile from the
-input sent to the JNet service. For instance, if a sequence is known to include
-a large loop insertion, hiding that section prior to submitting the JNet
-prediction can produce different results. In some cases, these secondary
-structure predictions can be more reliable for sequence on either side of the
-insertion\footnote{This, of course, cannot be guaranteed.}. Prediction results
-returned from the service will be mapped back onto the visible parts of the
-sequence, to ensure a single frame of reference is maintained in your analysis.
-
-
\exercise{Secondary Structure Prediction}{
\label{secstrpredex}
{\sl Note: The annotation panel can get quite busy during this exercise. Try
hiding some annotations rows by right clicking
the mouse in the annotation label panel and select the ``Hide this row'' option.
-The Annotations dropdown menu on the alignment wndow also provides options for
-reording and hiding autocalculated and sequence associated annotation. }
+The Annotations dropdown menu on the alignment window also provides options for
+reordering and hiding autocalculated and sequence associated annotation. }
\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by
clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$
{\bf Homework:} Go back to the last step of exercise \ref{annotatingalignex} and
follow the instructions to view the Jalview annotations file created from the annotations
-generated by the JPred server for your sequence.}
+generated by the JPred server for your sequence.
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2.25in]{images/jpred1.pdf}
+\includegraphics[width=3in]{images/jpred2.pdf}
+\caption{{\bf Secondary Structure Prediction} Status (left) and results (right)
+windows for JPred predictions. }
+\label{jpred}
+\end{center}
+\end{figure}
+
+
+Jpred is launched in the same way as the other web services. Select {\sl Web
+Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JPred
+Secondary Structure Prediction}\footnote{JNet is the Neural Network based
+secondary structure prediction method that the JPred server uses.} from the
+alignment window menu (Figure \ref{jpred}).
+A status window opens to inform you of the progress of the job. Upon completion, a new alignment window opens and the Jpred
+predictions are included as annotations. Consult the Jpred documentation for
+information on interpreting these results.
+
+\subsection{Hidden Columns and JPred Predictions}
+\label{hcoljnet}
+Hidden columns can be used to exclude parts of a sequence or profile from the
+input sent to the JNet service. For instance, if a sequence is known to include
+a large loop insertion, hiding that section prior to submitting the JNet
+prediction can produce different results. In some cases, these secondary
+structure predictions can be more reliable for sequence on either side of the
+insertion\footnote{This, of course, cannot be guaranteed.}. Prediction results
+returned from the service will be mapped back onto the visible parts of the
+sequence, to ensure a single frame of reference is maintained in your analysis.
\section{Protein Disorder Prediction}
\label{protdisorderpred}
thresholding (described in Section \ref{featureschemes}) can be used to
highlight differences in disorder prediction across aligned sequences.
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=5in]{images/disorderpred.pdf}
-\caption{{\bf Shading alignment by sequence disorder}. Alignment of Interleukin IV homologs coloured with Blosum62 with protein disorder prediction sequence features overlaid, shaded according to their score. Borderline disordered regions appear white, reliable predictions are either Green or Brown depending on the type of disorder prediction. }
-\label{alignmentdisorder}
-\end{center}
-\end{figure}
\subsection{Navigating Large Sets of Disorder Predictions}
range(s) of residues predicted as disordered, and annotation rows gives
raw value for each residue. Values over 0.1204 indicates disorder.
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5in]{images/disorderpred.pdf}
+\caption{{\bf Shading alignment by sequence disorder}. Alignment of Interleukin IV homologs coloured with Blosum62 with protein disorder prediction sequence features overlaid, shaded according to their score. Borderline disordered regions appear white, reliable predictions are either Green or Brown depending on the type of disorder prediction. }
+\label{alignmentdisorder}
+\end{center}
+\end{figure}
+
\subsubsection{RONN {\sl a.k.a.} Regional Order Neural Network}
\href{http://www.strubi.ox.ac.uk/RONN}{RONN} employs an approach
known as the `bio-basis' method to predict regions of disorder in
\exstep{Apply the IUPred disorder prediction method. 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. {\sl Note how well the disordered regions predicted by each method agree
-with the structure.}}}
+with the structure.}}
+\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
\chapter{DNA and RNA Sequences}
\label{dnarna}
git://source.jalview.org / jalview-manual.git / commitdiff