\vspace{2in}
-Manual Version 1.6
+Manual Version 1.6
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-12th May 2016
+9th June 2016
\end{center}
\end{center}
\end{figure}
+\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
+$\Rightarrow$ Preferences } dialog box.} calculate a set of automatic annotation
+rows which are shown below the alignment. For nucleotide sequence alignments,
+only an alignment consensus row will be shown, but for amino acid sequences,
+alignment quality (based on BLOSUM 62) and physicochemical conservation will
+also be shown. Conservation is calculated according to Livingstone and
+Barton\footnote{{\sl ``Protein Sequence Alignments: A Strategy for the
+Hierarchical Analysis of Residue Conservation." } Livingstone C.D. and Barton
+G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}.
+Consensus is the modal residue (or {\tt +} where there is an equal top residue).
+The inclusion of gaps in the consensus calculation can be toggled by
+right-clicking on the the Consensus label and selecting {\sl Ignore Gaps in
+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.
+
+
\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
{\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the
annotation. } }
+
\section{Importing Features from Databases}
\label{featuresfromdb}
Jalview supports feature retrieval from public databases either directly or {\sl
desired, add a short description (``One of four Iron binding Cysteines") and press OK. The features will then appear on the sequences. } \exstep{Roll the mouse cursor over the new features. Note that the position given in the tool tip is the residue number, not the column number. To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at column 95. Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
}
\exstep{
-Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
+Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature
+Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
\exstep{Select {\sl View $\Rightarrow$ Feature Settings\ldots} from the
alignment window menu. The Sequence Feature Settings window will appear. Move
this so that you can see the features you have just created. Click the check
now displayed. Close the sequence feature settings box by clicking OK or
Cancel.} }
-\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.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=1.3in]{images/annots1.pdf}
-\includegraphics[width=2in]{images/annots2.pdf}
-\caption{{\bf Creating a new annotation row.} Annotation rows can be reordered by dragging them to the desired place.}
-\label{newannotrow}
-\end{center}
-\end{figure}
-
-To create a new annotation, first select all the positions to be annotated on the appropriate row. Right-clicking on this selection brings up the context menu which allows the insertion of graphics for secondary structure ({\sl Helix} or {\sl Sheet}), text {\sl Label} and the colour in which to present the annotation (Figure \ref{newannot}). On selecting {\sl Label} a dialogue box will appear, requesting the text to place at that position. After the text is entered, the selection can be removed and the annotation becomes clearly visible\footnote{When annotating a block of positions, the text can be partly obscured by the selection highlight. Pressing the [ESC] key clears the selection and the label is then visible.}. Annotations can be coloured or deleted as desired.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2in]{images/annots3.pdf}
-\includegraphics[width=2in]{images/annots4.pdf}
-\includegraphics[width=2in]{images/annots5.pdf}
-\caption{{\bf Creating a new annotation.} Annotations are created from a selection on the annotation row and can be coloured as desired.}
-\label{newannot}
-\end{center}
-\end{figure}
-
-\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. 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. } }
-
\chapter{Multiple Sequence Alignment}
\label{msaservices}
Sequences can be aligned using a range of algorithms provided by JABA web
using the `Algorithm ordering' entry within the {\sl Calculate $\Rightarrow$
Sort } sub menu.
+\subsubsection{Realignment}
+The re-alignment option is currently only supported by ClustalW and Clustal
+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
+provided by ClustalW in this case is effectively a simple form of profile
+alignment.
+
+
\begin{figure}[htbp]
\begin{center}
\parbox[c]{1.5in}{\includegraphics[width=1.5in]{images/ws1.pdf}}
\end{center}
\end{figure}
-\subsubsection{Realignment}
-The re-alignment option is currently only supported by ClustalW and Clustal
-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
-provided by ClustalW in this case is effectively a simple form of profile
-alignment.
-\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}.
-Furthermore, each contiguous segment of sequences will be aligned independently
-(resulting in a number of alignment `subjobs' appearing in the status window).
-Finally, the results of each subjob will be concatenated with the hidden regions
-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
-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
N-terminal region.}
}
+\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}.
+Furthermore, each contiguous segment of sequences will be aligned independently
+(resulting in a number of alignment `subjobs' appearing in the status window).
+Finally, the results of each subjob will be concatenated with the hidden regions
+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
+columns can be used to preserve existing parts of an alignment whilst the
+visible parts are locally refined.
+
\subsection{Customising the Parameters used for Alignment}
\subsubsection{What is PCA?}
Principal components analysis is a technique for examining the structure of
complex data sets. The components are a set of dimensions formed from the
-measured values in the data set, and the principle component is the one with the
+measured values in the data set, and the principal component is the one with the
greatest magnitude, or length. The sets of measurements that differ the most
-should lie at either end of this principle axis, and the other axes correspond
+should lie at either end of this principal axis, and the other axes correspond
to less extreme patterns of variation in the data set.
In this case, the components are generated by an eigenvector decomposition of
the matrix formed from the sum of pairwise substitution scores at each aligned
in Jalview's built in documentation.\footnote{See
\url{http://www.jalview.org/help/html/calculations/pca.html}.}
+
+\exercise{Principal Component Analysis}{ \exstep{Load the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa} }
+\exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}.
+A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible.
+Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window.
+Note that clicking on points in the plot will highlight them on the alignment. }
+\exstep{ Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$
+Neighbour Joining Using BLOSUM62}. A new tree window will appear.
+Click on the tree window. Careful selection of the tree partition location will divide the alignment into a number of groups,
+each of a different colour.
+Note how the colour of the sequence ID label matches both the colour of
+the partitioned tree and the points in the PCA plot.} }
+
\subsubsection{The PCA Viewer}
-PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principle
+PCA analysis can be launched from the {\sl Calculate $\Rightarrow$ Principlal
Component Analysis} menu option. {\bf PCA requires a selection containing at
least 4 sequences}. A window opens containing the PCA tool (Figure \ref{PCA}).
Each sequence is represented by a small square, coloured by the background
keys or the scroll wheel of the mouse (if available). A tool tip appears if the
cursor is placed over a sequence. Sequences can be selected by clicking on them.
[CTRL]-Click can be used to select multiple sequences.
+
+Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$
+Show Labels} menu option, and the plot background colour changed {\sl via} the
+{\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical
+representation of the PCA plot can be exported as an EPS or PNG image {\sl via}
+the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
+
\begin{figure}[hbtp]
\begin{center}
\includegraphics[width=2in]{images/PCA1.pdf}
\end{center}
\end{figure}
-Labels will be shown for each sequence by toggling the {\sl View $\Rightarrow$
-Show Labels} menu option, and the plot background colour changed {\sl via} the
-{\sl View $\Rightarrow$ Background Colour..} dialog box. A graphical
-representation of the PCA plot can be exported as an EPS or PNG image {\sl via}
-the {\sl File $\Rightarrow$ Save As $\Rightarrow$ \ldots } submenu.
-\exercise{Principle Component Analysis}{ \exstep{Load the alignment at
-\textsf{http://www.jalview.org/examples/exampleFile.jar} and press [ESC] to clear any selections. Alternatively, select {\sl Select $\Rightarrow$ Undefine Groups} to remove all groups and colourschemes. } \exstep{Select the menu option {\sl Calculate $\Rightarrow$ Principle Component Analysis}. A new window will open. Move this window so that the tree, alignment and PCA viewer window are all visible. Try rotating the plot by clicking and dragging the mouse on the plot in the PCA window. Note that clicking on points in the plot will highlight them on the alignment and tree. }
-\exstep{ Click on the tree window. Careful selection of the tree partition
-location will divide the alignment into a number of groups, each of a different
-colour. Note how the colour of the sequence ID label matches both the colour of
-the partitioned tree and the points in the PCA plot.
-} }
\subsubsection{PCA Data Export}
Although the PCA viewer supports export of the current view, the plots produced
} \parbox[c]{3in}{\centerline{
\includegraphics[width=2.5in]{images/pca_vmenu.pdf} }}
+\subsection{Tree Based Conservation Analysis}
+\label{treeconsanaly}
+
+Trees reflect the pattern of global sequence similarity exhibited by the
+alignment, or region within the alignment, that was used for their calculation.
+The Jalview tree viewer enables sequences to be partitioned into groups based
+on the tree. This is done by clicking within the tree viewer window. Once subdivided, the
+conservation between and within groups can be visually compared in order to
+better understand the pattern of similarity revealed by the tree and the
+variation within the clades partitioned by the grouping. The conservation based
+colourschemes and the group associated conservation and consensus annotation
+(enabled using the alignment window's {\sl View $\Rightarrow$ Autocalculated
+Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
+can help when working with larger alignments.
\exercise{Trees}{
\exstep{Ensure that you have at least 1G memory available in Jalview
(\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{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
}
-\subsection{Tree Based Conservation Analysis}
-\label{treeconsanaly}
-
-Trees reflect the pattern of global sequence similarity exhibited by the
-alignment, or region within the alignment, that was used for their calculation.
-The Jalview tree viewer enables sequences to be partitioned into groups based
-on the tree. This is done by clicking within the tree viewer window. Once subdivided, the
-conservation between and within groups can be visually compared in order to
-better understand the pattern of similarity revealed by the tree and the
-variation within the clades partitioned by the grouping. The conservation based
-colourschemes and the group associated conservation and consensus annotation
-(enabled using the alignment window's {\sl View $\Rightarrow$ Autocalculated
-Annotation $\Rightarrow$ Group Conservation} and {\sl Group Consensus} options)
-can help when working with larger alignments.
-
\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. }
{\sl Note: You may want to save the alignment and tree as a project file, since
it is used in the next few exercises. } }
+
\subsection{Redundancy Removal}
The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function, but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater than the current threshold are highlighted in black. The [Remove] button can then be used to delete these sequences from the alignment as an edit operation\footnote{Which can usually be undone. A future version of Jalview may allow redundant sequences to be hidden, or represented by a chosen sequence, rather than deleted.}.
\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}{
-
-\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc}). In
-the alignment window, you may need to deselect groups using Esc key.}
-\exstep{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 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}
colourschemes can then be used to reveal any associated pattern of sequence
variation across the whole alignment.
-\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
-$\Rightarrow$ Preferences } dialog box.} calculate a set of automatic annotation
-rows which are shown below the alignment. For nucleotide sequence alignments,
-only an alignment consensus row will be shown, but for amino acid sequences,
-alignment quality (based on BLOSUM 62) and physicochemical conservation will
-also be shown. Conservation is calculated according to Livingstone and
-Barton\footnote{{\sl ``Protein Sequence Alignments: A Strategy for the
-Hierarchical Analysis of Residue Conservation." } Livingstone C.D. and Barton
-G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}.
-Consensus is the modal residue (or {\tt +} where there is an equal top residue).
-The inclusion of gaps in the consensus calculation can be toggled by
-right-clicking on the the Consensus label and selecting {\sl Ignore Gaps in
-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 via the context menu linked to the
% annotation row; but they are only created on loading an alignment. If they are
% Sequence logos can be enabled by default for all new alignments {\sl via} the
% Visual tab in the Jalview desktop's preferences dialog box.
+\section{Pairwise Alignments}
+Jalview can calculate optimal pairwise alignments between arbitrary
+sequences {\sl via} the {\sl Calculate $\Rightarrow$ Pairwise Alignments\ldots} menu option.
+Global alignments of all pairwise combinations of the selected sequences are performed and the results returned in a text box.
+
+
+
+\exercise{Remove Redundant Sequences}{
+
+\exstep{Re-use or recreate the alignment and tree which you worked with in the
+tree based conservation analysis exercise (exercise \ref{consanalyexerc}). In
+the alignment window, you may need to deselect groups using Esc key.}
+\exstep{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 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.}
+}
+
\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})}
the tree groups made in the previous exercise.}
}
-\subsection{Other Calculations}
-
-
-\subsubsection{Pairwise Alignments}
-
-Jalview can calculate optimal pairwise alignments between arbitrary sequences {\sl via} the {\sl Calculate $\Rightarrow$ Pairwise Alignments\ldots} menu option. Global alignments of all pairwise combinations of the selected sequences are performed and the results returned in a text box.
-
\begin{figure}[]
\begin{center}
\includegraphics[width=4in]{images/pairwise.pdf}
\end{center}
\end{figure}
-\pagebreak[2]
\chapter{Working with 3D structures}
\label{3Dstructure}
git://source.jalview.org / jalview-manual.git / blobdiff