{\Huge
-Jalview 2.9.0b2}
+Jalview 2.10.0}
\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.
in your web browser. Launch Jalview by clicking on the
pink `Launch Jalview' Desktop button in the top right hand corner. This
will download and open a jalview.jnlp webstart file.}
-\exstep {Dialogue boxes
+\exstep {Dialog 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 {\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
\exstep{To deactivate the opening of the 4 demo sequences during the launch, go
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. A `Preference'
-dialogue box opens, untick the box adjacent to the `Open file' entry in the
+dialog box opens, untick the box adjacent to the `Open file' entry in the
`Visual' preferences tab.
Click {\sl OK} to save the preferences.}
\exstep{Launch another Jalview workbench from the web site by clicking on the
may want to move this from the downloads folder to another folder.
Opening from the jnlp file will allow Jalview to be launched offline.
-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}.}
}
the alignments and analysis windows at once, then use the {\sl Window
$\Rightarrow$ Close All} option from the Jalview desktop.
-{\bf \em{Warning: make sure you have saved your work because this cannot be
+{\bf \em{Warning: Make sure you have saved your work because this cannot be
undone!}} }
\parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
}}
Documentation window. Select topic from the navigation panel on the left hand side or use the
Search tab to select specific key words.
-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
+{\sl\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}.}
}
\section{Loading Sequences and Alignments}
by Jalview. The way to read sequences from these documents is to select the
data from the document and copy it to the clipboard. There are two ways to
do this. One is to right-click on the desktop background, and select the
-`Paste to new alignment' option in the menu that appears. The other is to select
+`Paste to new window' option in the menu that appears. The other is to select
{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the
-main menu, and paste the sequences into the textbox window that will appear
-(Figure \ref{loadtext}). In both cases, presuming that they are in the right
-format, Jalview will happily read them into a new alignment window.
+main menu, paste the sequences into the text window that will appear, and select
+{sl New Window} (Figure \ref{loadtext}). In both cases, presuming that they are
+in the right format, Jalview will happily read them into a new alignment window.
%[fig 8]
\begin{figure}[htbp]
\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 the {\sl Paste to New Window} menu
+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.
-(iii) 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.}
+\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
+$\Rightarrow$ Fetch Sequence(s)...} from the Desktop. The {\sl Select Database
+Retrieval Source} dialog will open showing all the database sources. Select the
+{\bf PFAM seed} database and click {\sl OK}.
+
+(ii)Once a source has been selected, the {\sl New
+Sequence Fetcher} window will open. Enter the accession number {\bf PF03460}
+and click {\sl OK}.
+An alignment of about 174 sequences should load.}
\exstep{These can be viewed using the Overview window accessible from {\sl View
$\Rightarrow$ Overview Window.}
Several database IDs can be loaded by using semicolons to separate them.}
-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
-}
+{\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}} }
\section{Saving Sequences and Alignments}
\label{savingalignments}
-\subsection{Saving Alignments} Jalview allows the
-current sequence alignments to be saved to file so they can be restored at a
-later date, passed to colleagues or analysed in other programs. From the
-alignment window menu select {\sl File $\Rightarrow$ Save As} and a dialog box
+\subsection{Saving Alignments} Jalview allows alignments to be saved to file
+in a variety of formats so they can be restored at a later date, passed to
+colleagues or analysed in other programs. From the alignment window menu select {\sl File $\Rightarrow$ Save As} and a dialog box
will appear (Figure \ref{savealign}). You can navigate to an appropriate
directory in which to save the alignment. Jalview will remember the last filename
and format used to save (or load) the alignment, enabling you to quickly save
-the file during or after editing by using the {\sl File $\Rightarrow$ Save} entry.
+the file during or after editing by using the {\sl File $\Rightarrow$ Save}
+entry. The {\sl File $\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into
+other documents or web servers.
-Jalview offers several different formats in which an alignment can be saved. The
-jalview format (.jar) is the only format which will preserve the colours,
-groupings and other additional information in the alignment. The other formats
+Jalview offers several different formats in which an alignment can be saved.
+Of these, only the jalview project format (.jar or .jvp) will preserve the colours, 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
-$\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into
-other documents or web servers.
+Unfortunately, as far as we are aware only Jalview can read Jalview
+project files.
%[fig 10]
\begin{figure}[htbp]
just a single alignment (e.g. because you have calculated trees or multiple
different alignments) then save your work as a Jalview Project
file (.jvp).\footnote{Tip: Ensure that you have allocated plenty of memory to
-Jalview when working with large alignments in Jalview projects. See Section \protect
-\ref{memorylimits} above for how to do this.}
+Jalview when working with large alignments in Jalview projects. See Section
+\ref{memorylimits} for how to do this.}
From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save
dialog box will appear. Loading a project will restore Jalview to exactly the
view at which the file was saved, complete with all alignments, trees,
\exstep{Close all windows and then load the project {\sl via} the {\sl File
$\Rightarrow$ Load Project} menu option. Observe how all the windows and
positions are exactly as they were when they were saved. }
-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
+{\bf See the video at: \url{http://www.jalview.org/Help/Getting-Started}.}
}
{\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]
$\Rightarrow$ Group $\Rightarrow$ Edit name and description of
current group}\footnote{In earlier versions of Jalview, this entry was variously
`Group', `Edit Group Name', or `JGroupXXXXX' (Where XXXXX was some serial
-number).} then enter a name for the group in the dialogue box which appears.
+number).} then enter a name for the group in the dialog box which appears.
By default the new group will have a box drawn around it. The appearance of the group can be changed (see Section \ref{colours} below). This group will stay defined even when the selection is removed.
\exercise{Making Selections and Groups}{
\label{exselect}
\exstep{Close windows.
+
Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM seed} database).
-Choose a residue and place the mouse
+}
+\exstep{Selecting an arbitrary region. Choose a residue and place the mouse
cursor on it (residue information will show in alignment window status
bar).
-Click and drag the mouse to create a selection. As you drag, a red box
-will `rubber band' out to
+Click and drag the mouse to the bottom-right to create a selection. As you drag,
+a red box will `rubber band' out to
show the extent of the selection.
Release the mouse
button and a red box borders the selected region.
background and a red box appears around the selected sequence.
Hold down [SHIFT] and click another sequence ID a few positions above or below.
Note how the selection expands to include all the sequences between the two positions on which you clicked.
-Hold down [CTRL] and then click on several sequences ID's both selected and
+Hold down [CTRL] and then click on several sequences' IDs - both selected and
unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are
individually deselected.}
-\exstep{ Select column by clicking on the Alignment Ruler. Note whole
-column is highlighted with a red box.
-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{ Select columns by clicking on the Alignment Ruler. Note
+that the selected column is marked with a red box.
+Hold down [SHIFT] and click a column beyond. Note the selection expands to
+include all the sequences between the two positions on which you clicked.}
+
\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, try manually editing the
+alignment before clicking the {\sl New Window} button. This opens the
+edited alignment in a new alignment window.} {\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}
% more? change colouring style. set border colour.
}
sequences, use hold [SHIFT], and select two sequences separated by
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}.}
+{\bf See the video 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 can select either {\sl
+Reveal Sequences} to reveal the hidden sequences that were clicked, or {\sl
+Reveal All}.
}
\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
with (Sequence ID name )}. To reveal these hidden sequences, right click on the
Sequence ID and in the context menu select {\sl Reveal All}.}
-{\bf A video about this exercise is available on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
\section{Introducing and Removing Gaps}
The alignment view provides an interactive editing interface, allowing gaps to be inserted or deleted to the left of any position in a sequence or sequence group. Alignment editing can only be performed whilst in keyboard editing mode (entered by pressing [F2]) or by clicking and dragging residues with the mouse when [SHIFT] or [CTRL] is held down (which differs from earlier versions of Jalview).
+
+\subsection{Undoing Edits}
+Alignment edits can be undone {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
+alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
+with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
+{\sl Undo} function only works for edits to the alignment or sequence ordering.
+Colouring of the alignment, showing and hiding of sequences or modification of
+annotation that only affect the alignment's display cannot
+be undone.
+
\subsection{Locked Editing}
\label{lockededits}
The Jalview alignment editing model is different to that used in other alignment
% % better idea to introduce hiding sequences, and use the invert selection, hide
% others, to simplify manual alignment construction
+\subsection{Editing in Cursor mode}
+Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
+pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
+under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
+press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
+or [SHIFT]-[SPACE] (both keys held down together).
+
+Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
+have everything unselected by pressing ESC. The gap under the cursor will be
+removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
+will be deleted up to the number specified. To delete gaps from all sequences of
+a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
+together). Note that the deletion will only occur if the gaps are in the same
+columns in all sequences in the selected group, and those columns are to the
+right of the selected residue.
+
+\newpage
+
\exercise{Editing Alignments}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
alignment available at
\href{http://www.jalview.org/examples/exampleFile.jar}
{http://www.jalview.org/examples/exampleFile.jar}.
+
+{\sl {\bf Mac Users: Please use the Apple or [CMD] key in place of [CTRL]
+for key combinations such as [CTRL]-A.} }
+
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
backwards and replay the edits you have made.}
}
-\subsection{Editing in Cursor mode}
-Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
-pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
-under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
-press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
-or [SHIFT]-[SPACE] (both keys held down together).
-
-Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
-have everything unselected by pressing ESC. The gap under the cursor will be
-removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
-will be deleted up to the number specified. To delete gaps from all sequences of
-a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
-together). Note that the deletion will only occur if the gaps are in the same
-columns in all sequences in the selected group, and those columns are to the
-right of the selected residue.
\exercise{Keyboard Edits}
{This continues on from the previous exercise, and recreates the final part of the example ferredoxin
insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}. The top five sequences are
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
-with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
-{\sl Undo} function only works for edits to the alignment or sequence ordering.
-Colouring of the alignment, showing and hiding of sequences or modification of
-annotation cannot be undone.
-
\chapter{Colouring Sequences and Figure Generation}
\label{colouringfigures}
\section{Colouring Sequences}
\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: Before you begin this exercise, ensure that the {\sl Apply Colour
+To All Groups} flag is not selected in {\sl Colour} menu in the alignment window.
+% patch needed for 2.10 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 dialog 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 See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
\subsubsection{User Defined}
-This dialogue allows the user to create any number of named colour schemes at will. Any residue may be assigned any colour. The colour scheme can then be named. If you save the colour scheme, this name will appear on the Colour menu (Figure \ref{usercol}).
+This dialog allows the user to create any number of named colour schemes at will. Any residue may be assigned any colour. The colour scheme can then be named. If you save the colour scheme, this name will appear on the Colour menu (Figure \ref{usercol}).
\begin{figure}[htbp]
\exercise{User Defined Colour Schemes}{
-\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialogue window will open.}
+\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialog window will open.}
\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{ 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 dialog 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 See the video 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
-\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.
-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.
- In Chapter \ref{alignanalysis}, you will find
-descriptions and exercises on building and displaying trees, PCA analysis,
-alignment redundancy removal, pairwise alignments and alignment conservation
-analysis.
-Chapter \ref{wkwithstructure} introduces the structure visualization
-capabilities of Jalview.
-Chapter \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS protein disorder prediction
-services are introduced in Chapter \ref{protdisorderpred}.
-Chapter \ref{workingwithnuc} describes functions and visualization techniques relevant
-to working with nucleotide sequences, coding region annotation and nucleotide
-sequence alignments.
-Chapter \ref{jvwebservices} introduces the various web based services
-available to Jalview users, and Chapter \ref{jabaservices} explains how to
-configure the Jalview Desktop for access to new JABAWS servers.
+\newpage
+
+\section{Summary - the rest of the manual}
+
+The first few chapters have covered the basics of Jalview operation: from
+starting the program, importing, exporting, selecting, editing and colouring
+aligments, to the generation of figures for publication, presentation and web
+pages.
+
+The remaining chapters in the manual cover:
+
+\begin{list}{$\circ$}{}
+\item{Chapter \ref{featannot} covers the creation, manipulation and visualisation
+of sequence and alignment annotation, and retrieval of sequence and feature data
+from databases.}
+\item {Chapter \ref{msaservices} explores the range of multiple alignment
+programs offered via Jalview's web services, and introduces the use of
+AACon for protein multiple alignment conservation analysis.}
+\item {Chapter \ref{alignanalysis} introduces Jalview's built in tools for
+multiple sequence alignment analysis, including trees, PCA, and alignment
+conservation analysis. }
+\item {Chapter \ref{3Dstructure} demonstrates the structure visualization
+capabilities of Jalview.}
+\item {Chapter \ref{proteinprediction} introduces protein sequence based
+secondary structure and disorder prediction tools, including JPred.}
+\item {Chapter \ref{dnarna} covers the special functions and
+visualization techniques for working with RNA alignments and protein coding
+sequences.}
+\item {Chapter \ref{jvwebservices} provides instructions on the
+installation of your own Jalview web services.}
+\end{list}
\chapter{Annotation and Features}
\label{featannot}
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.
\subsection{Creating User Defined Annotation}
To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}).
-A dialogue box appears. Enter the label to use for this row and a new row will appear.
+A dialog box appears. Enter the label to use for this row and a new row will appear.
To create a new annotation, first select all the positions to be annotated on the appropriate row.
Right-clicking on this selection brings up the context menu which allows the insertion of graphics for secondary structure ({\sl Helix} or {\sl Sheet}),
-text {\sl Label} and the colour in which to present the annotation (Figure \ref{newannot}). On selecting {\sl Label} a dialogue box will appear,
+text {\sl Label} and the colour in which to present the annotation (Figure \ref{newannot}). On selecting {\sl Label} a dialog box will appear,
requesting the text to place at that position. After the text is entered, the selection can be removed and the annotation becomes clearly
visible\footnote{When annotating a block of positions, the text can be partly obscured by the selection highlight. Pressing the [ESC] key clears
the selection and the label is then visible.}. Annotations can be coloured or deleted as desired.
\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 dialog 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{
Right click at this selection and select {\sl Label} from the context menu.
Enter ``Fe" in the box and click {\sl OK}. Right-click on the selection again
and select {\sl Colour}.
-Choose a colour from the colour chooser dialogue
+Choose a colour from the colour chooser dialog
and click {\sl OK}. Press [ESC] to remove the selection.
+
+{\sl Note: depending on your Annotation sort settings, your newly
+created annotation row might 'jump' to the top or bottom of the annotation
+panel. Just scroll up or down to find it again - the column you marked will
+still be selected. }
+
}
\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 {\sl OK}. A new line showing the
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
% }
\subsection{Creating Sequence Features}
-Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialogue box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.
+Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialog box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.
\begin{figure}[htbp]
\begin{center}
present it is usually necessary to customise the display. Jalview allows the
display, colour, rendering order and transparency of features to be modified
{\sl via} the {\sl View $\Rightarrow$ Feature Settings\ldots} menu option. This
-brings up a dialogue window (Figure \ref{custfeat}) which allows the
+brings up a dialog window (Figure \ref{custfeat}) which allows the
visibility of individual feature types to be selected, colours changed (by
clicking on the colour of each sequence feature type) and the rendering order
modified by dragging feature types to a new position in the list. Dragging the
iron binding so we will create them as features. Navigate to column 97, sequence 1.
Select the entire column by clicking in the ruler bar. Then right-click on the selection
to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}.
-A dialogue box will appear.
+A dialog box will appear.
}
\exstep{
Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
}
\exstep{
-Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature
+Add a similar feature to column 102. When the feature dialog box appears, clicking the Sequence Feature
Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
\exstep{Select {\sl View $\Rightarrow$ Feature Settings\ldots} from the
alignment window menu. The Sequence Feature Settings window will appear. Move
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 See the video 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 See the video 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 See the video 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 See the video 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 See the video 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 See the video 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
\subsection{Viewing Structures}
\label{viewAllStructures}
-The structure viewer can be launched in two ways from the sequence ID context
+The structure viewer is launched from the sequence ID context
menu. To view a particular structure associated with a sequence in the
-alignment, simply select it from popup menu's associated structures submenu in
-{\sl Structure $\Rightarrow$ View Structure $\Rightarrow$ $<$PDB ID$>$}. The
-second way is most useful if you want to view all structural data available for
-a set of sequences in an alignment. If any of the {\bf currently selected}
-sequences have structures associated, the {\sl Structure } submenu of the
-sequence ID popup menu will include an option to {\sl View {\bf N}
-structures}. Selecting this option will open a new structure view containing
+alignment, select the sequence and right click the mouse to open context
+menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} opens a Structure Chooser dialog box.
+The second way is most useful if you want to view all structural data available for
+a set of sequences in an alignment. Select all the sequence ids in the sequence
+ID panel and right click the mouse to open context
+menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$}. If any of
+the {\bf currently selected} sequences have structures associated they will
+appear in the Structure Chooser dialog box. The structures can be ranked by
+different parameters, 'Best Quality' is defaul option. Select the
+structures required and click {\sl View} to open a structure viewer containing
the associated structures superposed according to the alignment.
-In both cases, each structure to be displayed will be downloaded or loaded from
+The structure to be displayed will be downloaded or loaded from
the local file system, and shown as a ribbon diagram coloured according to the
associated sequence in the current alignment view (Figure \ref{structure}
(right)). The structure can be rotated by clicking and dragging in the structure
\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 See the video 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
-\url{http://www.jalview.org/training/Training-Videos}.} }
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.} }
\subsection{Superimposing Structures}
\label{superposestructs}
Jalview can employ Jmol's 3D fitting routines\footnote{See
\href{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}
for more information.} to recreate 3D structure superpositions based on the
-correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view happens automatically if a
-structure is added to an existing Jmol display using the {\sl Structure
-$\Rightarrow$ View PDB Structure $\Rightarrow$ ..}. A new Jmol view containing
-superposed structures can also be created using the {\sl Structure
-$\Rightarrow$ View all {\bf N} PDB Structures} option (when {\bf {\sl N}}
-$>$ 1) if the current selection contains two or more sequences with associated
+correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view
+ happens automatically if a
+structure is added to an existing Jmol display using
+{\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} to open the Structure Chooser dialog box.
+Select structures required and select {\sl View}. A new Jmol view
+opens containing superposed structures if the current selection contains two or more sequences with associated
structures.
\subsubsection{Obtaining the RMSD for a Superposition}
directly compared.
In order to recompute a superposition after changing a view or editing the
-alignment, select the {\sl Jmol $\Rightarrow$ Align sequences } menu option. The {\sl
-Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
+alignment, select the {\sl Jmol $\Rightarrow$ Align Structures} menu option.
+The {\sl Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
associated alignments and views are to be used to create the set of
correspondences. This menu is useful when composing complex superpositions
involving multi-domain and multi-chain complexes, when correspondences may be
prediction on the first sequence in the set (that is, the one that appears first in the alignment window).
\end{list}
Jpred is launched in the same way as the other web services. Select {\sl Web
-Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
+Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet
Secondary Structure Prediction}\footnote{JNet is the Neural Network based
secondary structure prediction method that the JPred server uses.} from the
alignment window menu (Figure \ref{jpred}).
Disordered regions in proteins were classically thought to correspond to
``linkers'' between distinct protein domains, but disorder can also play a role in
-function. The {\sl Web Services $\Rightarrow$ Disorder} menu in the alignment window
+function. The {\sl Web Service $\Rightarrow$ Disorder} menu in the alignment window
allows access to protein disorder prediction services provided by the configured
JABAWS servers.
\exercise{Secondary Structure Prediction}{
\label{secstrpredex}
\exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by
-clicking on the sequence ID. Then select {\sl Web Services $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction}
+clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction}
from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear.
Note that the number of sequences in the results window is many more than in the original alignment as
JNet performs a PSI-BLAST search to expand the prediction dataset. The results
\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 / blobdiff