{\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.
-12th September 2015
+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.
will download and open a jalview.jnlp webstart file.}
\exstep {Dialogue boxes
will open and ask if you want to open the jalview.jnlp file as the file is an application downloaded from the
-Internet, click Open. (Note you may be asked to update Java, if you agree then
-it will automatically update the Java software). As Jalview opens, four demo
+Internet, click {\sl Open}. (Note you may be asked to update Java, if you agree
+then it will automatically update the Java software). As Jalview opens, four demo
Jalview windows automatically load.}
\exstep {If
you are having trouble, it may help changing the browser you are using, as the browsers and
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. The tick the `Open file' entry of `Visual'
preferences tab, type in the URL of the sequence you want to load.
+
+
As the jalview.jnlp file launches Jalview on your desktop, you
may want to move this from the downloads folder to another folder.
Opening from the jnlp file will allow Jalview to be launched offline.
\exstep{Find the Overview Window, {\sl Views
$\Rightarrow$ Overview Window} and open it. Move around the
alignment by clicking and dragging the red box in the overview window.}
-\exstep{Return to the alignment window. Look at the status bar (lower left hand
-corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
+\exstep{Return to the alignment window, look at the status bar (lower left
+hand corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
sequence and residue under the cursor.}
-\exstep{Press [F2] key, or [Fn]/[F2] on Mac, to enter Cursor mode. Use
+\exstep{Press [F2] key, or [Fn]-[F2] on Mac, to enter Cursor mode. Use
the direction keys to move the cursor around the alignment.}
\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
two different positions if gaps are inserted into the sequence. Move to sequence 5,
-column 13 by typing {\bf 1 3 , 5 [RETURN]}.}
+column 13 by typing {\bf 1 3 , 5} [RETURN].}
{\bf Note:} To view Jalview's comprehensive on-line help documentations select
-{\sl Help} on desktop menu, clicking on {\sl Documentation} will open a
+{\sl Help} in desktop menu, clicking on {\sl Documentation} will open a
Documentation window. Select topic from the navigation panel on the left hand side or use the
Search tab to select specific key words.
\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}
$\Rightarrow$ Close All}. Then drag the alignment.fa file from the desktop and
drop it onto the Jalview window, the alignment should open.
-Test the differences
+(ii) Test the differences
between (a) dragging the sequence onto the Jalview desktop and (b)
dragging the sequence onto an existing alignment window.
-(ii) Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
+(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.)
+download directory and open it in a text editor.)}
-(iii) 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 Paste to new alignment option.
+\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 Window} to new
+alignment option.
-(iv) In the text editor, copy the sequence text from
+(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). In the Desktop menu, select {\sl File
+$\Rightarrow$ Copy} menu option).
+
+(iii) In the 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.}
-\exstep{{\bf Loading sequences from Public Database:} Select {\sl File
+
+\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.
-Press database selection button (top of the dialog box), this opens
-another window called Select Database Retrieval Source showing all the database
-sources.
-
-Select the {\bf PFAM seed} database and click {\sl OK}, then enter the accession
-number {\bf PF03460} and click {\sl OK}. An alignment of about 174 sequences should
-load. These can be viewed using the Overview window accessible from {\sl View
+called Select Database Retrieval Source showing all the database
+sources. Select the {\bf PFAM seed} database and click {\sl OK}.
+
+(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
$\Rightarrow$ Overview Window.}
Several database IDs can be loaded by using semicolons to separate them.}
{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
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.
location into which to save the alignment and select your preferred format. All
formats except {\sl Jalview } jvp can be viewed in a normal text editor (e.g.
Notepad) or in a web browser.
-Enter a file name and click {\sl Save}.
-
-Check this file by closing all windows and opening it with Jalview, or by
+Enter a file name and click {\sl Save}.}
+\exstep{Check this file by closing all windows and opening it with Jalview, or by
browsing to it with your web browser.}
-\exstep{ Repeat the previous step saving the files in different file formats.}
+\exstep{Repeat the previous steps saving the files in different file formats.}
\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}.
Select and copy this alignment to the clipboard using the textbox menu options
{\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}.
{\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).
+\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.
Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
-to complete the selection. Note to clear the selection press the {\bf[ESC]}
+to complete the selection. Note to clear the selection press the [ESC]
key.}
\exstep{To create a group from the selected the region, click the
right mouse button when mouse is on the selection, this opens a
-pop-up menu in the alignment window.
+context menu in the alignment window.
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
} menu and select {\sl Percentage Identity}.
This will turn the selected region into a group and colour it accordingly.}
\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences in
the alignment by clicking on their Sequence ID label. Note how the group expands
-to include newly selected sequences, and the `Percentage Identity' colouring changes. }
+to include newly selected sequences, and the Percentage Identity colouring changes. }
\exstep{ Another way to resize the group is by using the mouse to click and drag
the right-hand edge of the selected group.}
-\exstep{The current selection can be exported and saved by right clicking
-on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an
-output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
+\exstep{The current selection can be exported and saved by right clicking the
+mouse when on the text area to open the Sequence ID context menu. Follow the
+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 to import the file into 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}.}
+\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.
}
\exercise{Reordering the Alignment}{
\exstep{Close all windows in Jalview from desktop menu. Load the ferredoxin
-alignment (e.g. the PFAM domain PF03460 from PFAM seed).
+alignment using the PFAM domain PF03460 from PFAM seed database.
Select one of the sequence in the sequence ID panel, use the up and down
arrow keys to alter the sequence's position in the alignment. (Note that
this will not work in cursor mode)}
\exstep{To select and move multiple
sequences, use hold [SHIFT], and select two sequences separated by
-one or more un-selected sequences repeat using [CTRL]. Note how multiple
-sequences are grouped together when they are re-ordered using the up and down arrow keys.}
+one or more un-selected sequences, repeat using the [CTRL] key. Note how
+multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.}
{\bf A video about this exercise is available on the Jalview website
at \url{http://www.jalview.org/training/Training-Videos}.}
}
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.}
-\exstep{Select a region of the alignment, and experiment with the `Hide all but
-selected region' function in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
-\exstep{Select some sequences, pick one to represent the rest by hovering
+\exstep{Select a region of the alignment, and experiment with the {\sl Hide all
+but selected region} option in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
+but selected region.}} \exstep{Select some sequences, pick one to represent the rest by hovering
the mouse over this sequence. Bring up the Sequence ID context menu by right
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
with (Sequence ID name )}. To reveal these hidden sequences, right click on the
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 pressing the [CMD] key instead of [CTRL].}
\exstep{ Load the URL
\textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the
ferredoxin alignment from PF03460.}
\exstep{ Select the first 7 sequences, and press H to hide them (or right click
-on the sequence IDs to open the sequence ID pop-up menu, and select {\sl Hide
+on the sequence IDs to open the sequence ID context menu, and select {\sl Hide
Sequences}).}
\exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
Insert another gap at column 47 in all sequences in the same way.}
\exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by
-inserting two additional gaps after the gap at column 47: First press [ESC] to
+inserting two additional gaps after the gap at column 47. First press [ESC] to
clear the selection, then hold [SHIFT] and click and drag on the G and move it
two columns to the right.}
column 38.
Press {\sl 34C [BACKSPACE] 38C 2 [SPACE]}. Delete three gaps at column 44 and
insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are
-now aligned.}
-}
+now aligned.}}
+
\section{Undoing Edits}
Jalview supports the undoing of edits {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
\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 {\sl 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{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.}
\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{
and click {\sl 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
+ context menu. You will be prompted for a label. Enter ``B" and press {\sl 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 Export Annotation dialog box that will open, select the Jalview format and click
-the [To Textbox] button.
+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
\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
+\exstep{Add an additional helix somewhere along the row by editing the file and
re-importing it.
{\sl Hint: Use the Export Annotation function to view what helix annotation looks like in
a Jalview annotation file.}}
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
A window will open giving the job status. After a short time, a second window will open
with the results of the alignment.}
\exstep{Return to the first sequence alignment window by clicking on
- the window, and repeat using {\sl ClustalO} (Omega) and {\sl MAFFT} (from the
- {\sl Web Service $\Rightarrow$ Alignment} menu) on the same initial alignment. Compare them and
- you should notice small differences. }
+ the window, and repeat using {\sl ClustalO} (Omega) and {\sl MAFFT}, from the
+ {\sl Web Service $\Rightarrow$ Alignment} menu, using the same initial
+ alignment.
+ Compare them and you should notice small differences. }
\exstep{Select the last three sequences in the MAFFT alignment, and de-align them
with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect these
sequences. Then submit this view for re-alignment with {\sl ClustalO}.}
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
\exstep {If you wish,
select and hide a few more columns in the N-terminal region, and submit the alignment to the
service again and explore the effect of local alignment on the non-homologous parts of the
-N-terminal region.}
+N-terminal region.}
+{\bf A video about this exercise is available on the Jalview website at
+\url{http://www.jalview.org/training/Training-Videos}.}
}
\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 $\Rightarrow$ Principle Component Analysis}.
+\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.
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 $\Rightarrow$
+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.
Note how the colour of the sequence ID label matches both the colour of
-the partitioned tree and the points in the PCA plot.} }
+the partitioned tree and the points in the PCA plot.}
+{\bf A video about this exercise is available on the Jalview website at
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
\begin{figure}[hbtp]
\begin{center}
can help when working with larger alignments.
\exercise{Trees}
-{Ensure that you have at least 1G memory available in Jalview
-(Either start with this link:
+{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 ``latest official build'' row in the table, go to the
-``Webstart'' column, click on ``G2''.)
+in the table, go to ``latest official build'' row and ``Webstart'' column, click on ``G2''.)}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
-Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
-\exstep{Click on the tree window, a cursor will appear. Note that placing
-this cursor divides the tree into a number of groups by colour.
+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
+{\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 using
- different methods.} \exstep{Select from sequence 2 column 60 to sequence 12 column 123. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear. It can be seen that the tree contains 11 sequences. It has been coloured according to the already selected groups from the first tree and is calculated purely from the residues in the selection.
+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. }}
+alignment for the calculation of trees.
+
+{\bf A video about this exercise is available on the Jalview website at
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
\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 $\Rightarrow$
\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.
-
+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}. }
+{\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
+{\bf A video about this exercise is available on the Jalview website 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}
-, and set {\sl Conservation } shading threshold at around 20. }
+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
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.}
-
+window. }
\exstep {You may find it easier to browse the alignment if you first uncheck the
-{\sl Annotations $\Rightarrow$ Show Annotations} option, and open the Overview Window
-within the View menu to aid navigation.}
+{\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 few exercises. } }
+{\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
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
\subsection{Redundancy Removal}
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
+\exstep{From the tree window, select {\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})}
+tree based conservation analysis exercise (exercise \ref{consanalyexerc}).}
\exstep{In the {\sl View} menu in the alignment window, select {\sl New View} to
create a new view. Ensure the annotation panel is displayed ({\sl Show annotation} in {\sl Annotations} menu). Enable the
display of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
-Autocalculated Annotation } submenu in the sequence alignment window.}
+Autocalculated Annotation } submenu in the alignment window.}
\exstep{Displaying the sequence
logos will make it easier to see the different residue populations within each
group. Activate the logo by right clicking on the Consensus annotation row to
open the context menu and select the {\sl Show Logo} option.}
\exstep{In the column alignment ruler, select a column exhibiting about 50\%
conservation that lies within the central conserved region of the alignment.
-(Column 74 is used in \href{https://youtu.be/m-PjynicXRg}{the Tree video}.}
+(Column 74 is used in \href{https://youtu.be/m-PjynicXRg}{the Tree video}).}
\exstep{Subdivide the alignment
according to this selection using {\sl Select $\Rightarrow$ Make groups for selection}.}
\exstep{Re-order the alignment according to the new groups that have been
\exstep{Select another column exhibiting about 50\% conservation
overall, and subdivide the alignment further. Note that the new groups
inherit the names of the original groups, allowing you to identify the
-combination of mutations that resulted in the subdivision.
-}
+combination of mutations that resulted in the subdivision.}
\exstep{Clear the groups, and try to subdivide the alignment using two
non-adjacent columns.
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
+\url{http://www.jalview.org/training/Training-Videos}.}
}
\begin{figure}[]
\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
{\sl File $\Rightarrow$ View Mapping} from the structure viewer menu.
A new window opens showing the residue by residue alignment between the sequence and the structure.}
\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file.
-Once the file is saved, open the location in your file browser (or explorer window) and drag the PDB file that you just saved on
-to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu).
+Once the file is saved, open the location in your file browser (or explorer
+window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu).
Verify that you can open and view the associated structure from the sequence ID
-pop-up menu's {\sl 3D Structure } submenu in the new alignment window.}
+context menu's {\sl 3D Structure } submenu in the new alignment window.}
\exstep{In the Jmol window, right click on the structure window and explore the
menu options. Try to change the style of molecular display - for example by
using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.}
-\exstep{In the alignment window, use the {\sl File $\Rightarrow$ Save As .. }
+\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.}}
+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
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
\exercise{Setting Chimera as the default 3D Structure Viewer}{\label{viewingchimera}
Jalview supports molecular structure
\exstep{Close the Jalview program, from the
{\sl Desktop menu} select {\sl Jalview $\Rightarrow$ Quit Jalview}. Then reopen
Jalview, Chimera should open as the default viewer.}
-{\sl Note: The Jmol structure viewer sits within the Jalview desktop; however
+{\sl Note: The Jmol structure viewer sits within the Jalview desktop. However
the Chimera structure viewer sits outside the Jalview desktop and a Chimera
-view window sits inside the Jalview desktop.} }
+view window sits inside the Jalview desktop.}
+
+{\bf A video about this exercise is available on the Jalview website at
+\url{http://www.jalview.org/training/Training-Videos}.} }
\subsection{Superimposing Structures}
\label{superposestructs}
IDs associated with the FER1\_MAIZE sequence.}
\exstep{Once discovery has completed, use the {\sl
View PDB Structure} submenu to view one of the PDB file associated with
-FER1\_MAIZE (eg. 3B2F), Jalview will give you the option of aligning the
+FER1\_MAIZE (eg. 3B2F). Jalview will give you the option of aligning the
structure to the one already open. To superimpose the structure associated with FER1\_MAIZE with the one
associated with FER1\_SPIOL, press the {\sl Yes} button.
{\sl The Jmol view will update to show both structures, and one will be
-moved on to the other. If this doesn't happen, use the Align function in the Jmol submenu}}
-\exstep{Create a new view on the alignment, and hide all but columns 121
+moved on to the other. If this doesn't happen, use the Align function in the
+Jmol submenu}.} \exstep{Create a new view on the alignment, and hide all but columns 121
through to 132.}
\exstep{Use the {\sl Jmol} submenu to
recompute the superposition using just columns 121-132 of the alignment
-(The easiest way to achieve this is to select column 121-132 and in the View
+(The easiest way to achieve this is to select column 121-132, and in the View
menu selected ``All but selected region'' from the Hide options).
{\sl Note how the molecules shift position when superposed using a short part of
the small section and with the whole alignment.}
\exstep{The RMSD report can be
viewed by right clicking the mouse on Jmol window, and select ``Show" and
-``Measurements".
-
-Which view do you think give the best 3D
+``Measurements". Which view do you think give the best 3D
superposition, and why ?} }
\subsubsection{Colouring Complexes}
\exstep{Download the PDB file at
\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop.
-
This is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA
server.}
\exstep{Launch the Jalview desktop and ensure you have at least 256MB of
free memory available.
+
{\sl Use the following webstart link:
\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}
{\sl Alternatively in the Development section of the Jalview web site
Reference Annotation} option.
{\bf All} the JNet predictions for the sequences will now be visible in the
-original alignment window.
+original alignment window.}
{\sl Note: The annotation panel can get quite busy and it may be
helpful to hide some of the annotations rows, by right clicking the mouse in
the annotation label panel and select ``Hide this row'' option in the context
-menu}.} }
+menu}. }
\begin{figure}[htbp]
\begin{center}
\exercise{Protein Disorder Prediction}{
%\label{protdispredex}
-\exstep{Open the alignment at
+\exstep{Open the alignment at:
\url{http://www.jalview.org/tutorial/interleukin7.fa}. } also available at
IDs} to retrieve all the PDB structures for the sequences.}
\exstep{Open and align
-the structures for all sequences. {\sl Hint: see \ref{viewAllStructures} to see
-how to do this.}}
+the structures for all sequences. ({\sl Hint: see \ref{viewAllStructures} to see
+how to do this.})}
\exstep{Compare the disorder predictions to the structure data by mapping any
available temperature factors to the alignment {\sl via} the {\sl Sequence ID
\exstep{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.
+
Do the two methods agree with the structure ?}}
\chapter{DNA and RNA Sequences}
\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).}
{
\exstep{Use the sequence fetcher to retrieve EMBL record D49489.}
\exstep{Ensure that {\sl View $\Rightarrow$ Show Sequence Features} is checked and change the
-alignment view format to Wrapped mode so the distinct exons can be seen.}
+alignment view format to {\sl Wrapped} mode so the distinct exons can be seen.}
\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots}
window {\sl View $\Rightarrow$ Features setting}
and fetch features for D49489 from the Uniprot reference server,
\exercise{Viewing RNA Structures}
{ \label{viewingrnaex}
-\exstep{Import RF00162 from Rfam (Full) using Fetch sequence(s) option in File
-menu.}
+\exstep{Import RF00162 from Rfam (Full) using {\sl Fetch sequence(s)} option in
+{\sl File} menu.}
\exstep{Select {\sl Colour by RNA Helices} to shade the alignment by
the secondary structure annotation provided by Rfam.}
Base Pair probabilities. Explore how editing the alignment affects the consensus
calculation.}
-\exstep{Import 2GIS from PDB database using Fetch sequence(s) option.}
+\exstep{Import 2GIS from PDB database using {\sl Fetch sequence(s)} option.}
\exstep{Click on a sequence in Sequence ID panel and select {\sl Structure
$\Rightarrow$ View Structure $\Rightarrow$ 2GIS}, to view the structure in Jmol
window. Click on different residues and located them in the sequence alignment window.}
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 / blobdiff