{\Huge
-Jalview 2.9.0b2}
+Jalview 2.10.00}
\vspace{0.5in}
{\huge
\vspace{2in}
-Manual Version 1.7
+Manual Version 1.8
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-28th September 2016
+7th October 2016
\end{center}
The Jalview Desktop in this version
provides access to protein and nucleic acid sequence, alignment and structure
databases, and includes the Jmol\footnote{ Provided under the LGPL licence at
-\url{http://www.jmol.org}} viewer for molecular structures, and the VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of RNA secondary structure. A
-Distributed Annotation System (DAS) client\footnote{jDAS - released under Apache license (v2.0) at \url{http://code.google.com/p/jdas}} which facilitates the retrieval and display of third party sequence
-annotation in association with sequences and any associated structure. It also
-provides a graphical user interface for the multiple sequence alignment, conservation analysis and protein disorder prediction methods provided as {\bf Ja}va {\bf B}ioinformatics
-{\bf A}nalysis {\bf W}eb {\bf S}ervices (JABAWS). JABAWS\footnote{released under GPL at \url{http://www.compbio.dundee.ac.uk/jabaws}} is a system for running bioinformatics programs that you can download and run on your own machine or cluster, or install on compute clouds.
+\url{http://www.jmol.org}} viewer for molecular structures, and the VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of
+RNA secondary structure. It also
+provides a graphical user interface for the multiple sequence alignment, conservation analysis
+and protein disorder prediction methods provided as {\bf Ja}va {\bf B}ioinformatics
+{\bf A}nalysis {\bf W}eb {\bf S}ervices (JABAWS). JABAWS\footnote{released under GPL at \url{http://www.compbio.dundee.ac.uk/jabaws}} is a system for
+running bioinformatics programs that you can download and run on your own machine or cluster, or install on compute clouds.
\subsection{Jalview's Capabilities}
% TODO add references to appropriate sections for each capability described here.
the Jalview Desktop's webservices is given in Section \ref{jvwebservices}, and
the alignment and secondary structure prediction services are described
in detail in Sections \ref{msaservices} and \ref{protsspredservices}. Section \ref{featannot} details the creation and visualization of sequence
-and alignment annotation, and the retrieval of sequences and annotation from
-databases and DAS Servers. Section \ref{workingwithnuc} discusses
+and alignment annotation. Section \ref{workingwithnuc} discusses
specific features of use when working with nucleic acid sequences, such as translation and linking to protein
coding regions, and the display and analysis of RNA secondary structure.
\label{fetchseq}
Jalview can retrieve sequences and sequence alignments from the public databases
housed at the European Bioinformatics Institute, including Uniprot, Pfam, Rfam
-and the PDB, as well as any DAS sequence server registered at the configured DAS
-registry. Jalview's sequence fetching capabilities allow you to avoid having to
+and the PDB. Jalview's sequence fetching capabilities allow you to avoid having to
manually locate and save sequences from a web page before loading them into
Jalview. It also allows Jalview to gather additional metadata provided by the
source, such as annotation and database cross-references.
press OK. Jalview will then attempt to retrieve them from the chosen database.
Example queries are provided for some databases to test that a source is
operational, and can also be used as a guide for the type of accession numbers
-understood by the source.\footnote{Most DAS sources support {\em range queries}
-that can be used to download just a particular range from a sequence database
-record.}
+understood by the source.
% [fig 9]
\begin{figure}[htbp]
\begin{center}
\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 {\sl Paste} to new alignment option.
+background by right-clicking and selecting {\sl Paste to New Window} to new
+alignment option.
(ii) In the text editor, copy the sequence text from
alignment.fa into the clipboard (usually {\sl via} the browser's {\sl Edit
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.}
+
\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
$\Rightarrow$ Fetch Sequence(s)...} from the Desktop to open up new window
-called New Sequence Fetcher.
-
-(ii) Press database selection button (top of the dialog box), this opens
-another window called Select Database Retrieval Source showing all the database
-sources.
+called Select Database Retrieval Source showing all the database
+sources. Select the {\bf PFAM seed} database and click {\sl OK}.
-(iii) Select the {\bf PFAM seed} database and click {\sl OK}, then enter the
+(ii)This opens another window called New Sequence Fetcher, 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
groupings and other additional information in the alignment. The other formats
produce text files containing just the sequences with no visualization information, although some
allow limited annotation and sequence features to be stored (e.g. AMSA).
-Unfortunately only Jalview program can read Jalview files. The {\sl File
+Unfortunately only Jalview can read Jalview files. The {\sl File
$\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into
other documents or web servers.
{\bf To clear (unselect) the selection press the [ESC] (escape) key.}
\subsection{Selecting Arbitrary Regions}
-To select part of an alignment, place the mouse at the top left corner of the region you wish to select. Press and hold the mouse button and drag the mouse to the bottom right corner of the chosen region then release the mouse button. A dashed red box appears around the selected region (Figure \ref{select}).
+To select part of an alignment, place the mouse at the top left corner of the region you wish to select. Press and hold the mouse button and drag the mouse to the bottom right corner of the chosen region then release the mouse button.
+A dashed red box appears around the selected region (Figure \ref{select}).
%[fig 12]
\begin{figure}[htbp]
Hold down [SHIFT] and click column beyond. Note the selection expands to include
all the sequences between the two positions on which you clicked.}
-\exstep{ To selecting arbitrary regions in alignment, place the mouse at the top
-left corner of the region you wish to select. Press and hold the mouse button.
-Drag the mouse to the bottom right corner of the chosen region and release the
-mouse button and a dashed red box appears around the selected region}
\exstep{Enter Cursor mode using [F2], or [Fn]-F2 for Macs.
Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
Press {\bf Q} to mark this position.
menus and pick an output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
\ldots} submenu.
}
-\exstep{Try manually editing the alignment.}
-\exstep{Import the group into a new alignment window by clicking the {\sl New
-Window} button.}
-{\bf A video about this exercise is available on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}
+\exstep{In the Alignment output window that opens, manually edit the
+alignment before clicking the {\sl New Window} button, this opens the
+edited alignment in a new alignment window.} {\bf A video about this exercise is
+available on the Jalview website at \url{http://www.jalview.org/training/Training-Videos}.}
% more? change colouring style. set border colour.
}
All Sequences.}) }
\exstep{
Repeat the process but use a non-contiguous set of sequences. Note that when
-multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
+multiple regions are hidden you may prefer to select {\sl
+Reveal Sequences} rather than {\sl Reveal All} option.
}
\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
alignment available at
\href{http://www.jalview.org/examples/exampleFile.jar}
{http://www.jalview.org/examples/exampleFile.jar}.
+
+{\sl Note: If you are using OSX, and a key combination - such as [CTRL]-A - does
+ not work, then try the [CMD] key instead of [CTRL].}
+
Remember to use [CTRL]-Z to undo an edit, or the {\sl File $\Rightarrow$
Reload } function to revert the alignment back to the original version if you
want to start again.
-
-{\sl Note: If you are using OSX, and a key combination - such as [CTRL]-A - does
- not work, then try the [CMD] key instead of [CTRL].}
\exstep{ Load the URL
\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
\exercise{Colouring Alignments}{
\label{color}
-\exstep{Ensuring that the {\sl Apply Colour To All Groups} flag is not selected in {\sl View} menu in the alignment window.
-This must be turned {\sl off} specifically as it is on by default.}
+Note: Ensuring that the {\sl Apply Colour To All Groups} flag is not
+selected in {\sl Colour} menu in the alignment window.
+This must be turned {\sl off} specifically as it is on by default.
+
\exstep{Open a sequence alignment, for example the PFAM domain PF03460 in PFAM
seed database. Select the alignment menu option {\sl Colour $\Rightarrow$
ClustalX} and note the colour change. Now try all the other colour schemes in the {\sl Colour} menu.
\exstep{Keeping the same selection as before, colour the complete alignment except
the group using {\sl Colour $\Rightarrow$ Taylor}.
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
-Slide the selector from side to side and observe the changes in the alignment
-colouring in the selection and in the complete alignment.}
-{\bf A video about this exercise is available on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}
+Slide the selector in the Conservation Colour Increment dialogue box from side
+to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
+Note: Feature colours overlay residue colouring. The features colours can be
+toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}.
+
+{\bf A video about this exercise is
+available on the Jalview website at \url{http://www.jalview.org/training/Training-Videos}.}
}
\subsubsection{User Defined}
\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialogue window can now be closed.}
\exstep{The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
-{\bf A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.}} }
\section{Formatting and Graphics Output}
resolution.}
}
-The next chapters introduce Jalviews analysis features. Chapter \ref{featannot}
-describes the mechanisms provided by Jalview for interactive creation of sequence and alignment annotation, and how they can be displayed, imported and exported and used to reorder the alignment. Chapter
+The next chapters introduce Jalview's analysis features. Chapter \ref{featannot}
+describes the mechanisms provided by Jalview for interactive creation of sequence and alignment annotation, and how they can be displayed,
+imported and exported and used to reorder the alignment. Chapter
\ref{featuresfromdb} discusses the retrieval of database references and
establishment of sequence coordinate systems for the retrieval and display of
-features from databases and DAS annotation services.
+features from databases.
Chapter \ref{msaservices} describes how to use the range of multiple alignment
programs provided by JABAWS, and Chapter \ref{aacons} introduces JABAWS AACon
service for protein multiple alignment conservation analysis.
overlaid on the sequences and the alignment.
Generally speaking, annotations reflect properties of the alignment as a
whole, often associated
-with columns in the alignment. Whilst features are associated with specific residues in the sequence.
+with columns in the alignment. Features are often associated with specific
+residues in the sequence.
Annotations are shown below the alignment in the annotation panel, the
properties are often based on 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
+data sources. Webservices like JNet (see \ref{jpred} above) can be used to analyse a
given sequence or alignment and generate annotation for it.
-\section{Conservation, Quality and Conservation Annotation}
+\section{Conservation, Quality and Consensus Annotation}
\label{annotationintro}
Jalview automatically calculates several quantitative alignment annotations
which are displayed as histograms below the multiple sequence alignment columns.
-Conservation, quality and conservation scores are examples of dynamic
+Conservation, quality and consensus scores are examples of dynamic
annotation, so as the alignment changes, they change along with it.
The scores can be used in the hybrid colouring options to shade the alignments.
Mousing over a conservation histogram reveals a tooltip with more information.
\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}.
+bring up the context menu and select {\sl Add New Row}. A dialogue box will
+appear asking for {\sl Annotation Name} and {\sl Annotation Description}.
Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
}
\exstep{
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
+\label{viewannotfileex}
+{\sl Homework for after you have completed exercise \ref{secstrpredex}:}
+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
SEQUENCE\_REF statements surrounding the row specifying the sequence association for the
-annotation. } }
+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/}).
+Jalview supports feature retrieval from public databases.
It includes built in parsers for Uniprot and ENA (or EMBL) records retrieved
from the EBI. Sequences retrieved from these sources using the sequence fetcher (see
Section \ref{fetchseq}) will already possess features.
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.
+Databases}, which includes EMBL, Uniprot, the PDB, 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
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 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.}
-\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 labelled box at the top of the panel.
-
-\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.
-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{
-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
-}
-}
\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.
+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.
\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.
+contains a large number of sequences.
+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.
\subsection{Colouring Features by Score or Description
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,
by right clicking the mouse to bring up context menu.
-Select {\sl Web Services $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults} to
+Select {\sl Web Service $\Rightarrow$ 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
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.}
-{\bf A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.}
}
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.}
-{\bf A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.}
}
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 A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.}
}
can be set in Preferences using
{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
-{\bf A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.}
}
{\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 A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.}
}
both of the columns that you wish to use to subdivide the alignment.}}
\exstep{Switch back to the original view, and experiment with subdividing
the tree groups made in the previous exercise.}
-{\bf A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.}
}
\chapter{Working with 3D structures}
\label{3Dstructure}
-Jalview can interactively view 3D structure using Jmol or Chimera. Setting in
-the Structure window within Preferences determine whether Jmol or Chimera is
-the default choice of structure viewer.
+Jalview can interactively view 3D structure using Jmol or Chimera. Whether Jmol or Chimera is
+the default structure viewer of choice is set from {\sl Preferences}, go
+to {\sl Tools $\Rightarrow$ Preferences\ldots} and select either JMOL or
+CHIMERA in the {\sl Structure} tab.
% To review, Chapter \ref{featannot} describes the mechanisms provided by
% Jalview for interactive creation of sequence and alignment annotation, and how
\exstep{Right-click on the
sequence ID label of {\sl FER1\_SPIOL} to open
the context menu. Select {\sl 3D Structure}, this
-opens a Structure Chooser window, select { \sl 1A70} and click {\sl OK}.
+opens a Structure Chooser window, select { \sl 1A70} and click {\sl View}.
{\sl Note: the Structure Chooser interface
provides a smart technique for selecting PDB structures by queryingthe meta-data
of structures. Extra information can be including in this window by checking boxes
-in the ``Configure Displayed Columns'' tab}.
+in the columns of the ``Customise Displayed Options'' tab}.
% JBP Note: Bug JAL-1238 needs to be fixed ASAP
}
\exstep{By default the Jmol
\exstep{In the alignment window, 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.}
-{\bf A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.}
}
the Chimera structure viewer sits outside the Jalview desktop and a Chimera
view window sits inside the Jalview desktop.}
-{\bf A video about this exercise is available on the Jalview website at at
+{\bf A video about this exercise is available on the Jalview website at
\url{http://www.jalview.org/training/Training-Videos}.} }
\subsection{Superimposing Structures}
\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 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.
+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.
\begin{figure}[htbp]
\begin{center}
\label{dnadasfeatures}
\includegraphics[width=5in]{images/dnadasfeatures.pdf}
-\caption{Uniprot and PDB sum features retrieved {\sl via} DAS and mapped onto
+\caption{Uniprot and PDB sum features retrieved and mapped onto
coding regions of EMBL record V00488 (an earlier version of Jalview is shown
here).}
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
-in Section \ref{featuresfromdb}. A second type of one way service is provided
-by Jalview's DAS sequence feature retrieval system, which is described
-in Section \ref{dasfretrieval}.
+in Section \ref{featuresfromdb}.
% The final type of one way service are sequence
% and ID submission services.
% exemplified by the `Envision2 Services' provided
git://source.jalview.org / jalview-manual.git / commitdiff