-being observed within well defined regions of secondary structure or
-within regions of random coil. The initial signal is smoothed with a
-Savitzky-Golay filter, and its first order derivative
-computed. Residues for which the first order derivative is positive
-are designated as natively unstructured, whereas those with negative
-values are structured.
-
-{\bf Disordered region} sequence features are created marking mark range(s) of residues with positive first order derivatives, and
-\textbf{Globular Domain} features mark long stretches of order. \textbf{Dydx} annotation rows gives the first order derivative of smoothed score. Values above 0 indicates
-residue is disordered.
-
-\textbf{Smoothed Score and Raw Score} annotation rows give the smoothed and raw scores used to create the differential signal that
-indicates the presence of unstructured regions. These are hidden
-by default, but can be shown by right-clicking on the alignment
-annotation panel and selecting \textbf{Show hidden annotation}.
-
-\section{Features and Annotation}
-\label{featannot}
-Features and annotations are additional information that is overlaid on the sequences and the alignment. Generally speaking, annotations are associated with columns in the alignment. Features are associated with specific residues in the sequence.
-
-Annotations are shown below the alignment in the annotation panel, and often reflect properties of the alignment as a whole. The Conservation, Consensus and Quality scores are examples of dynamic annotation, so as the alignment changes, they change along with it. Conversely, sequence features are properties of the individual sequences, so they do not change with the alignment, but are shown mapped on to specific residues within the alignment.
-
-Features and annotation can be interactively created, or retrieved from external
-data sources. DAS (the Distributed Annotation System) is the primary source of
-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}
-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]
-\begin{center}
-\includegraphics[width=2in]{images/feature1.pdf}
-\includegraphics[width=2.5in]{images/feature2.pdf}
-\includegraphics[width=1.5in]{images/feature3.pdf}
-\caption{{\bf Creating sequence features.} Features can readily be created from selections via the context menu and are then displayed on the sequence. }
-\label{features}
-\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.
-
-\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
-present it is usually necessary to customise the display. Jalview allows the
-display, colour, rendering order and transparency of features to be modified
-{\sl via} the {\sl View $\Rightarrow$ Feature Settings\ldots} menu option. This
-brings up a dialogue window (Figure \ref{custfeat}) which allows the
-visibility of individual feature types to be selected, colours changed (by
-clicking on the colour of each sequence feature type) and the rendering order
-modified by dragging feature types to a new position in the list. Dragging the
-slider alters the transparency of the feature rendering. The Feature
-Settings dialog also includes functions for more advanced feature shading
-schemes and buttons for sorting the alignment according to the distribution of
-features. These capabilities are described further in sections
-\ref{featureschemes} and \ref{featureordering}.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=4in]{images/features4.pdf}
-\caption{{\bf Multiple sequence features.} An alignment with JPred secondary structure prediction annotation below it, and many sequence features overlaid onto the aligned sequences. The tooltip lists the features annotating the residue below the mouse-pointer.}
-\end{center}
-\end{figure}
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=4in]{images/features5.pdf}
-\caption{{\bf Customising sequence features.} Features can be recoloured, switched on or off and have the rendering order changed. }
-\label{custfeat}
-\end{center}
-\end{figure}
-
-\subsection{Sequence Feature File Formats}
-
-Jalview supports the widely used GFF tab delimited format\footnote{see
-http://www.sanger.ac.uk/resources/software/gff/spec.html} and its own Jalview
-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
-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.
-}
-\exstep{
-Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
-appropriate box. Click on the Feature Colour bar to change the colour if
-desired, add a short description (``One of four Iron binding Cysteines") and press OK. The features will then appear on the sequences. } \exstep{Roll the mouse cursor over the new features. Note that the position given in the tool tip is the residue number, not the column number. To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC] then insert a gap in sequence 3 at column 95. Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
-}
-\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.}
-\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
-box for ``Iron binding site" under {\sl Display} and note that display of this
-feature type is now turned off. Click it again and note that the features are
-now displayed. Close the sequence feature settings box by clicking OK or
-Cancel.} }
-
-\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 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.
-}
-\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.}
-}
-\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. } }
-
-\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/}).
-It includes built in parsers for Uniprot and EMBL records retrieved from the
-EBI. Sequences retrieved from these sources using the sequence fetcher (see
-Section \ref{fetchseq}) will already possess features.
-
-\subsection{Sequence Database Reference Retrieval}
-\label{fetchdbrefs}
-Jalview maintains a list of external database references for each sequence in
-an alignment. These are listed in a tooltip when the mouse is moved over the
-sequence ID when the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$
-Show Database Refs } option is enabled. Sequences retrieved using the sequence
-fetcher will always have at least one database reference, but alignments
-imported from an alignment file generally have no database references.
-
-\subsubsection{Database References and Sequence Coordinate Systems}
-
-Jalview displays features in the local sequence's coordinate system which is
-given by its `start' and `end'. Any sequence features on the sequence will be
-rendered relative to the sequence's start position. If the start/end positions
-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}
-
-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
-[Sequence ID] $\Rightarrow$ Sequence details \ldots} option from the popup menu.
-A similar option is provided in the {\sl Selection} sub-menu allowing you to
-obtain annotation for the sequences currently selected.
-
-\parbox[l]{3.4in}{
-The {\sl Sequence Details
-\ldots} option will open a window containing the same text as would be shown in
-the tooltip window, including any web links associated with the sequence. The
-text is HTML, and options on the window allow the raw code to be copied and
-pasted into a web page.}
-\parbox[c]{3in}{
-\centerline{\includegraphics[width=2.2in]{images/seqdetailsreport.pdf}}}
-
-\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
-Webservice $\Rightarrow$ Fetch DB References} sub-menu in the Alignment
-window. This menu allows you to query either the set of {\sl Standard
-Databases}, which includes EMBL, Uniprot, the PDB, and the currently selected
-DAS sequence sources, or just a specific datasource from one of the submenus.
-When one of the entries from this menu is selected, Jalview will use the ID
-string from each sequence in the alignment or in the currently selected set to
-retrieve records from the external source. Any sequences that are retrieved are
-matched against the local sequence, and if the local sequence is found to be a
-sub-sequence of the retrieved sequence then the local sequence's start/end
-numbering is updated. A new database reference mapping is created, mapping the
-local sequence to the external database, and the local sequence inherits any
-additional annotation retrieved from the database sequence.
-
-The database retrieval process terminates when a valid mapping is found for a
-sequence, or if all database queries failed to retrieve a matching sequence.
-Termination is indicated by the disappearance of the moving progress indicator
-on the alignment window. A dialog box may be shown once it completes which
-lists sequences for which records were found, but the sequence retrieved from
-the database did not exactly contain the sequence given in the alignment (the
-{\sl ``Sequence not 100\% match'' dialog box}).
-
-\exercise{Retrieving Database References}{
-\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.}
-\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.}
-\exstep{Now close all the windows and open the project again, and verify that the database references and sequence features are still present on the alignment}
-
-\exstep{View the {\sl Sequence details \ldots} report for the FER1\_SPIOL sequence and for the whole alignment. Which sequences have web links associated with them ?}
-
-}
-
-\subsection{Retrieving Features {\sl via} DAS}
-\label{dasfretrieval}
-Jalview includes a client to retrieve features from DAS annotation servers. To
-retrieve features, select {\sl View $\Rightarrow$ Feature Settings\ldots} from the alignment window menu. Select the {\sl DAS Settings} tab in the Sequence Feature Settings Window (Figure \ref{das}). A list of DAS sources compiled from the currently configured DAS registry\footnote{By default, this will be the major public DAS server registry maintained by the Sanger Institute: http://www.dasregistry.org} is shown in the left hand pane. Highlighting an entry on the left brings up information about that source in the right hand panel.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2.5in]{images/das1.pdf}
-\includegraphics[width=2.5in]{images/das2.pdf}
-\caption{{\bf Retrieving DAS annotations.} DAS features are retrieved using the {\sl DAS Settings} tab (left) and their display customised using the {\sl Feature Settings} tab (right).}
-\label{das}
-\end{center}
-\end{figure}
-
-Select appropriate DAS sources as required then click on {\sl Fetch DAS
-Features}. If you know of additional sources not listed in the configured
-registry, then you may add them with the {\sl Add Local Source} button. Use
-the {\sl Authority},{\sl Type}, and {\sl Label} filters to restrict the list
-of sources to just those that will return features for the sequences in the
-alignment.
-
-Following DAS feature retrieval, the {\sl Feature Settings} panel takes on a
-slightly different appearance (Figure \ref{das} (right)). Each data source is
-listed and groups of features from one data source can be selected/deselected
-by checking the labeled box at the top of the panel.
-
-
-\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}
-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}{
-\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. }
-% TODO this doesn't work ! \includegraphics[width=.3in]{images/link.pdf}
-
-\exstep{
-Select {\sl View $\Rightarrow$ Feature Settings\ldots} to reopen the Feature Settings window. All the loaded feature types should now be displayed. Those at the top of the list are drawn on top of those below, obscuring them in the alignment view where they overlap. Move the feature settings window so that the alignment is visible and uncheck some of the feature types by clicking the tick box in the display column. Observe how the alignment display changes. Note that unselected feature types do not appear in the tool tip.
-}
-\exstep{Reorder the features by dragging feature types up and down the order in the Feature Settings panel. e.g. Click on {\sl CHAIN} then move the mouse downwards to drag it below {\sl DOMAIN}. Note that {\sl DOMAIN} is now shown on top of {\sl CHAIN} in the alignment window. Drag {\sl METAL} to the top of the list. Observe how the cysteine residues are now highlighted as they have a {\sl METAL} feature associated with them.
-}
-
-\exstep{Press the {\sl Optimise Order} button. The features will be ordered according to increasing length, placing features that annotate shorter regions of sequence higher on the display stack.}
-
-\exstep{Select {\sl File $\Rightarrow$ Export Features\ldots} from the Alignment window. You can choose to export the retrieved features as a GFF file, or Jalview's own Features format.
-% TODO: describe working with features files and GFF
-}
-}
-
-\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
-of a particular type are the result of a specific type of database query or calculation. Here, they may also carry information within their textual description, or most commonly for calculations, a score related to the property being investigated. Jalview can shade sequence
-features using a graduated colourscheme in order to highlight these variations.
-In order to apply a graduated scheme to a feature type, select the `Graduated
-colour' entry in the Sequence {\sl Feature Type}'s popup menu, which is opened by
-right-clicking the {\sl Feature Type} or {\sl Color} in the {\sl Sequence Feature Settings} dialog box. Two types
-of colouring styles are currently supported: the default is quantitative
-colouring, which shades each feature based on its score, with the highest
-scores receiving the `Max' colour, and the lowest scoring features coloured
-with the `Min' colour. Alternately, you can select the `Colour by label'
-option to create feature colours according to the description text associated
-with each feature. This is useful for general feature types - such as
-Uniprot's `DOMAIN' feature - where the actual type of domain is given in the
-feature's description.
-
-Graduated feature colourschemes can also be used to exclude low or
-high-scoring features from the alignment display. This is done by choosing your
-desired threshold type (either above or below), using the drop-down menu in the
-dialog box. Then, adjust the slider or enter a value in the text box to set the
-threshold for displaying this type of feature.