\vspace{0.5in}
{\huge
-Manual and Introductory Tutorial }
+Manual and Introductory Tutorial }
\vspace{2.4in}
may want to move this from the downloads folder to another folder.
Opening from this file will allow Jalview to be launched offline.
-{\bf Help launching Jalview is available in a video on
-\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
-the website.}}
+{\bf Help launching Jalview is available in videos on the Getting Started page
+of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}}
\subsection{Getting Help}
\label{gettinghelp}
window. Select topic from the navigation panel on the left hand side or use the
Search tab to select specific key words
-{\bf Help navigating Jalview is available in a video on
-\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
-the website.}}
+{\bf Help navigating is available in videos on the Getting Started page
+of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}}
\subsection{The Find Dialog Box}
\label{searchfunction}
{\sl Window $\Rightarrow$ Close All} menu option from the Desktop.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
your web browser and {\bf save} the file to your desktop.
-
Open the file you have just saved in Jalview by selecting {\sl File
$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu and
selecting this file.
$\Rightarrow$ Overview Window.}.
Several database IDs
-or accession numbers can be loaded by using semicolons to separate them.}}
+or accession numbers can be loaded by using semicolons to separate them.}
+{\bf Help loading sequences is available in videos on the Getting Started page
+of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
+}
\subsection{Memory Limits}
\label{memorylimits}
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. } }
+positions are exactly as they were when they were saved. }
+{\bf Help saving sequences is available in videos on the Getting Started page
+of the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}}
\section{Selecting and Editing Sequences}
\exercise{Making Selections and Groups}{
\label{exselect}
-\exstep{Close all windows in Jalview.
-Load the ferredoxin alignment (PFAM
-ID PF03460 from PFAM seed database).
+\exstep{Close windows.
+Load the ferredoxin alignment (PF03460 from PFAM seed database).
Choose a residue and place the mouse
-cursor on it. Note residue information will show in alignment window status bar.
-Click and drag the mouse cursor to create a selection. As you drag, a red box
+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
show the extent of the selection.
Release the mouse
-button and a red box should border the selected region.
-Press [ESC] to clear the selection.}
+button and a red box borders the selected region.
+Press [ESC] to clear this.}
\exstep{ Select one sequence by clicking on
the sequence ID panel. Note that the sequence ID takes on a highlighted
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
unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are
individually deselected.}
\exstep{In the alignment output window, try manually editing the alignment,
importing group into a new alignment window by clicking the [New Window] button to import the
file into a new alignment window.}
-
+{\bf Additional help is available from videos on the Jalview website at \url{http://www.jalview.org/training/Training-Videos}.}
% more? change colouring style. set border colour.
}
\exstep{To select and move multiple
sequences, use hold [SHIFT] and [CTRL], and select two sequences separated by
one or more un-selected sequences. Note how multiple sequences are grouped
-together when they are re-ordered using the up and down arrow keys.} }
+together when they are re-ordered using the up and down arrow keys.}
+{\bf Additional help is available from videos on the Jalview website
+at \url{http://www.jalview.org/training/Training-Videos}.}}
\subsection{Hiding Regions}
the mouse over this sequence. Bring up the Sequence ID pop-up menu by right
clicking and then 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 pop-up menu select Reveal All.}}
+Sequence ID and in the pop-up menu select Reveal All.}
+{\bf Additional help is available from videos on the Jalview
+website at \url{http://www.jalview.org/training/Training-Videos}}}
\begin{figure}[htb]
\exercise{Viewing Structures}{\label{viewingstructex}
\exstep{Load the alignment at
\textsf{http://www.jalview.org/examples/exampleFile.jar}. Right-click on the
-sequence ID label for any of the sequences (e.g. {\sl FER1\_SPIOL}) to bring up
+sequence ID label of {\sl FER1\_SPIOL}, this brings up
the context menu. Select {\sl FER1\_SPIOL $\Rightarrow$ Structure $\Rightarrow$
Associate Structure with Sequence $\Rightarrow$ Discover
PDB IDs}. Jalview will now attempt to find PDB structures for the sequences in
\exstep{Select {\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). Verify that you can open and view the associated structure from the sequence ID pop-up menu's {\sl Structure } submenu in the new alignment window.}
-\exstep{Right click on the structure to bring up the Jmol window. Explore the menu options. Try to change the style of molecular display - by first 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{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.
+\exstep{Right click on the structure in the submenu and bring up the Jmol
+window.
+Explore the menu options. Try to change the style of molecular display - by first 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{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.}
}
the cartoon style, with other parts of the molecule drawn in wireframe. The Jmol
console, which has been opened after the superposition was performed, shows the
RMSD report for the superposition.
-Full information about the superposition is also output to the Jalview
+Full information about the superposition is also outputed to the Jalview
console.\footnote{The Jalview Java Console is opened from {\sl Tools
$\Rightarrow$ Java Console} option in the Desktop's menu bar} This output also
includes the precise atom pairs used to superpose structures.
\begin{center}
\includegraphics[width=5.5in]{images/fdxsuperposition.pdf}
\caption{{\bf Superposition of two ferredoxin structures.} The alignment on the
-left was used by jalview to superpose structures associated with the
+left was used by Jalview to superpose structures associated with the
FER1\_SPIOL and FER1\_MAIZE sequences in the alignment. Parts of each structure
used for superposition are rendered as a cartoon, the remainder rendered in
wireframe. The RMSD between corresponding positions in the structures before and
\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
IDs associated with the FER1\_MAIZE sequence.}
\exstep{Once discovery has completed, use the {\sl
-View PDB Structure} submenu to view the PDB file associated with FER1\_MAIZE.
+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 structure to the one already
open. To superimpose the structure associated with FER1\_MAIZE with the one
associated with FER1\_SPIOL, press the {\bf Yes} button.
\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.
+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
+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 two structures.}}
\exstep{Compare the initial and final RMSDs for superimposing molecules with
-the small section and with the whole alignment. Which view do you think give the
-best 3D superposition, and why ?} }
+the small section and with the whole alignment. (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
+superposition, and why ?} }
\subsection{Colouring Structure Data Associated with Multiple Alignments and
Views} Normally, the original view from which a particular structure view was
{\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}.}}
-\exstep{Retrieve the following
-{\bf full} PFAM alignments: PF02008, PF00145, PF01426 (make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.}
-\exstep{Drag the structure you downloaded in
+\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
+(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds})
+in the ``latest official build'' row in the table, go to the
+``Webstart'' column, click on ``G2''.}}
+\exstep{Retrieve the following {\bf full} PFAM alignments: PF02008, PF01426
+(make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.} \exstep{Drag the URL or file of the structure you downloaded in
step 1 onto one of the alignments to associate it with the mouse sequence in
that Pfam domain family.}
\exstep{For every DNMT1\_MOUSE sequence in the alignment, use the sequence
\exercise{Trees}{
-\exstep{Ensure that you have at least 1G memory available in Jalview (start with this link: \href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}).}
+\exstep{Ensure that you have at least 1G memory available in Jalview
+(Either start with this 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''.)}
\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}. A new tree window will appear.}
\exstep{Click on the tree window. A cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour. Place the cursor to give about 4 groups, then select {\sl Calculate $\Rightarrow$ Sort $\Rightarrow$ By Tree Order $\Rightarrow$ Neighbour Joining Tree using BLOSUM62 from ... }. The sequences are reordered to match the order in the tree and groups are formed implicitly.}
-\exstep{Select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using \% Identity}. A new tree window will appear. The group colouring makes it easy to see the diferences 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.
+\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.
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.
}
\exstep{Recover the {\sl Input Data} for the tree you just calculated from the {\sl File} menu. Check the {\sl Edit $\Rightarrow$ Pad Gaps } option is {\sl not} ticked, and insert one gap anywhere in the alignment. Now select {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ Neighbour Joining Using BLOSUM62}.
\exercise{Tree Based Conservation Analysis}{
\label{consanalyexerc}
\exstep{Load the PF03460 PFAM seed alignment using the sequence fetcher. Colour it with the {\sl Taylor colourscheme}, and apply {\sl Conservation } shading. }
-\exstep{Build a Neighbourjoining tree using BLOSUM62 and use the {\sl Sort Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.}
-\exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
+\exstep{Build a Neighbour joining tree using BLOSUM62 and use the {\sl Sort
+Alignment By Tree} option in the tree viewer submenu to order alignment using the calculated tree.} \exstep{Select a point on the tree to partition the alignment, and examine the variation in colouring between different groups.
-You may find it easier to browse the alignment if you first uncheck the {\sl View $\Rightarrow$ Show Annotations} option, and open the Overview Window to aid navigation.}
+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.}
\exstep{Try changing the colourscheme 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. } }
\exercise{Remove Redundant Sequences}{
\exstep{Re-use or recreate the alignment and tree which you worked with in the
-tree based conservation analysis exercise (exercise \ref{consanalyexerc})}
-\exstep{Open the Remove Redundancy dialog and adjust the threshold to 90\%. Remove the sequences that are more than 90\% similar under this alignment.}
+tree based conservation analysis exercise (exercise \ref{consanalyexerc}). In
+the alignment window, you may need to deselect groups using Esc key.}
+\exstep{In the Edit menu select Remove Redundancy to open the Redundancy
+threshold selection dialog. Adjust the redundancy threshold value, start
+at 50 and increase the value to 65. Sequences selected will change colour in the Sequence ID panel. Select ``Remove'' to
+remove the sequences that are more than 65\% similar under this alignment.}
\exstep{Select the Tree viewer's {\sl View $\Rightarrow$ Mark Unlinked Leaves} option, and note that the removed sequences are now prefixed with a * in the tree view.}
-\exstep{Use the [Undo] button on the dialog to recover the sequences. Note that the * symbols disappear from the tree display.}
+\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.}
}
Consensus is the modal residue (or {\tt +} where there is an equal top residue).
The inclusion of gaps in the consensus calculation can be toggled by
right-clicking on the the Consensus label and selecting {\sl Ignore Gaps in
-Consensus} from the context menu. Quality is a measure of the inverse likelihood
-of unfavourable mutations in the alignment. Further details on these
+Consensus} from the pop-up context menu located with consensus annotation row.
+Quality is a measure of the inverse likelihood of unfavourable mutations in the alignment. Further details on these
calculations can be found in the on-line documentation.
-These annotations can be hidden and deleted but are only created on loading an
-alignment. If they are deleted then the alignment should be saved and reloaded
-to restore them. Jalview provides a toggle to autocalculate a consensus sequence
-upon editing. This is normally selected by default, but can be turned off for
+These annotations can be hidden and deleted via the context menu linked to the
+annotation row; but they are only created on loading an alignment. If they are
+deleted then the alignment should be saved and then reloaded to restore them.
+Jalview provides a toggle to autocalculate a consensus sequence upon editing. This is normally selected by default, but can be turned off for
large alignments {\sl via} the {\sl Calculate $\Rightarrow$ Autocalculate
Consensus} menu option if the interface is too slow.
Group associated consensus and conservation annotation rows reflect the
sequence variation within a particular group. Their calculation is enabled
by selecting the {\sl Group Conservation} or {\sl Group Consensus} options in
-the {\sl View $\Rightarrow$ Autocalculated Annotation } submenu of the alignment
-window.
+the {\sl Annotation $\Rightarrow$ Autocalculated Annotation } submenu of the
+alignment window.
\subsubsection{Alignment and Group Sequence Logos}
\label{seqlogos}
\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})}
-\exstep{Create a new view, and ensure the annotation panel is displayed, and
-enable the display of {\sl Group Consensus} and the display of sequence
-logos to make it easier to see the different residue populations within each group.}
-\exstep{Select a column exhibiting about 50\% conservation that lies within the
-central conserved region of the alignment. Subdivide the alignment according to
+\exstep{In the View menu, create a new view. Ensure the annotation panel
+is displayed (Show annotation in 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. Then display of sequence
+logos to make it easier to see the different residue populations within each
+group. Activate logo by right clicking on the Consensus annotation row to open
+the pop-up 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. 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
defined. Click on the group annotation row IDs to select groups exhibiting a
\subsection{Remote Analysis Web Services}
Remote analysis services enable Jalview to use external computational
-facilities. There are curently three types of service - multiple sequence
+facilities. There are currently three types of service - multiple sequence
alignment, protein secondary structure prediction, and alignment analysis.
Many of these are provided by JABA servers, which are described at the end of
this section. In all cases, Jalview will construct a job based on the alignment
T-COFFEE is the slowest, but also the most accurate. ClustalW is historically
the most widely used. Muscle is faster than ClustalW and probably the most
accurate for smaller alignments and MAFFT is probably the best for large
-alignments, however Clustal Omega, which was released in 2011, is arguably the
-fastest and most accurate tool for protein multiple alignment.
+alignments, however {\bf Clustal Omega}, which was released in 2011, is
+arguably the fastest and most accurate tool for protein multiple alignment.
To run an alignment web service, select the appropriate method from the {\sl
Omega. When performing a re-alignment, Jalview submits the current selection to
the alignment service complete with any existing gaps. This approach is useful
when one wishes to align additional sequences to an existing alignment without
-any further optimisation to the existing alignment. The Re-alignment service
+any further optimisation to the existing alignment. The re-alignment service
provided by ClustalW in this case is effectively a simple form of profile
alignment.
in the input data prior to their display in a new window. This approach ensures
that 1) hidden column boundaries in the input data are preserved in the
resulting alignment - in a similar fashion to the constraint that hidden columns
-place on alignment editing (see Section \ref{lockededits}), and 2) hidden
+place on alignment editing (see Section \ref{lockededits} and 2) hidden
columns can be used to preserve existing parts of an alignment whilst the
visible parts are locally refined.
\exercise{Multiple Sequence Alignment}{
\exstep{ Close all windows and open the alignment at {\sf
http://www.jalview.org/tutorial/unaligned.fa}. Select {\sl
-Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}. A window will open giving the job status. After a short time, a second window will open with the results of the alignment.} \exstep{Select the first sequence set by clicking on the window and try running ClustalW and MAFFT (from the {\sl Web Service $\Rightarrow$ Alignment} menu) on 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 them and then submit the view for re-alignment with ClustalW.}
-\exstep{Use [CTRL]-Z to recover the alignment of the last three sequences in the MAFFT alignment. Once the ClustalW re-alignment has completed, compare the results of 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. Select {\sl Web Services $\Rightarrow$ 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 region in the result with the corresponding region of the original alignment. 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.}
+Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}.
+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 Clustal and MAFFT (from the {\sl Web
+ Service $\Rightarrow$ Alignment} menu) on 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 them and then
+submit the view for re-alignment with Clustal.}
+\exstep{Use [CTRL]-Z to recover the alignment of the last three sequences in the MAFFT alignment.
+Once the Clustal re-alignment has completed, compare the results of 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.
+Select {\sl Web Services $\Rightarrow$ 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
+region in the result with the corresponding region of the original alignment. 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.}
}
\label{protdisorderpred}
Disordered regions in proteins were classically thought to correspond to
-'linkers' between distinct protein domains, but disorder can also play a role in
+``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
allows access to protein disorder prediction services provided by the configured
JABAWS servers.
\label{protdispredex}
\exstep{Open the alignment at
-\url{http://www.jalview.org/tutorial/interleukin7.fa}. }
+\url{http://www.jalview.org/tutorial/interleukin7.fa}. } also available at
+
+
+\url{http://www.jalview.org/tutorial/training-materials/2014/Dundee/Oct/interleukin7.fa}
\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Services
$\Rightarrow$ Disorder Prediction } submenu.}
features file.
\exercise{Creating Features}{
-\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in iron binding so we will create them as features. Navigate to column 97, sequence 1. Select the entire column by clicking in the ruler bar. Then right-click on the selection to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}. A dialogue box will appear.
+\exstep{Open the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
+We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved in
+iron binding so we will create them as features. Navigate to column 97, sequence 1.
+Select the entire column by clicking in the ruler bar. Then right-click on the selection
+to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}.
+A dialogue box will appear.
}
\exstep{
Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
\end{figure}
\exercise{Annotating Alignments}{
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. Right-click on the annotation label for {\sl Conservation} to bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}. Enter ``Iron binding site" and click OK. A new, empty, row appears.
+\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.
+Right-click on the {\sl Conservation} annotation row to
+bring up the context menu and select {\sl Add New Row}. A dialogue box will appear asking for {\sl Label for annotation}.
+Enter ``Iron binding site" and click OK. A new, empty, row appears.
}
\exstep{
-Navigate to column 97. Select column 97 on the new annotation row. Right click on the selection and select {\sl Label} from the context menu. Enter ``Fe" in the box and click OK. Right-click on the selection again and select {\sl Colour}. Choose a colour from the colour chooser dialogue and click OK. Press [ESC] to remove the selection.
-}
-\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the context menu. You will be prompted for a label. Enter ``B" and press OK. A new line showing the sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet arrow.
-}
-\exstep{Right click on the annotation row that you just created. Select {\sl Export Annotation} and, in the {\bf Export Annotation} dialog box that will open, select the Jalview format and click the [To Textbox] button.
-
-The format for this file is given in the Jalview help. Press [F1] to open it, and find the ``Annotations File Format'' entry in the ``Alignment Annotations'' section of the contents pane. }
-
-\exstep{Export the file to a text editor and edit the file to change the name of the annotation row. Save the file and drag it onto the alignment view.}
-\exstep{Try to add an additional helix somewhere along the row by editing the file and re-importing it.
-{\sl Hint: Use the {\bf Export Annotation} function to view what helix annotation looks like in a jalview annotation file.}}
-\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...} function to export all the alignment's annotation to a file.}
-\exstep{Open the exported annotation in a text editor, and use the {\bf Annotation File Format} documentation to modify the style of the Conservation, Consensus and Quality annotation rows so they appear as several lines on a single line graph.
-{\sl Hint: You need to change the style of annotation row in the first field of the annotation row entry in the file, and create an annotation row grouping to overlay the three quantitative annotation rows.}
+Navigate to column 97. Move down and on the new annotation row called
+``Iron binding site, select column 97.
+Right click at this selection and select {\sl Label} from the context menu.
+Enter ``Fe" in the box and click OK. Right-click on the selection again and select {\sl Colour}.
+Choose a colour from the colour chooser dialogue
+and click OK. Press [ESC] to remove the selection.
+}
+\exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the
+ context menu. You will be prompted for a label. Enter ``B" and press OK. A new line showing the
+ sheet as an arrow appears. The colour of the label can be changed but not the colour of the sheet
+ arrow.
+}
+\exstep{Right click on the title text of annotation row that you just created.
+Select {\sl Export Annotation} and, in the {\bf Export Annotation} dialog box that will open, select the Jalview format and click
+the [To Textbox] button.
+
+The format for this file is given in the Jalview help. Press [F1] to open it, and find
+the ``Annotations File Format'' entry in the ``Alignment Annotations'' section of the contents
+pane. }
+
+\exstep{Export the file to a text editor and edit the file to change the name of the annotation
+row. Save the file and drag it onto the alignment view.}
+\exstep{Try to add an additional helix somewhere along the row by editing the file and
+re-importing it.
+{\sl Hint: Use the {\bf Export Annotation} function to view what helix annotation looks like in
+a Jalview annotation file.}}
+\exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...}
+function to export all the alignment's annotation to a file.}
+\exstep{Open the exported annotation in a text editor, and use the {\bf Annotation File Format}
+documentation to modify the style of the Conservation, Consensus and Quality annotation rows so
+they appear as several lines on a single line graph.
+{\sl Hint: You need to change the style of annotation row in the first field of the annotation
+row entry in the file, and create an annotation row grouping to overlay the three quantitative
+annotation rows.}
}
\label{viewannotfileex}\exstep{Recover or recreate the secondary structure
-prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export Annotation} function to view the Jnet secondary structure prediction annotation row. Note the {\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the annotation. } }
+prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export
+Annotation} function to view the Jnet secondary structure prediction annotation row. Note the
+{\bf SEQUENCE\_REF} statements surrounding the row specifying the sequence association for the
+annotation. } }
\section{Importing Features from Databases}
\label{featuresfromdb}
\exstep{Load the example alignment at http://www.jalview.org/tutorial/alignment.fa}
\exstep{Verify that there are no database references for the sequences by first
checking that the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ Show
-Database IDs} option is selected, and then mousing over each sequence's ID.}
+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.}
Jalview has limited knowledge of the capabilities of the programs that
are made available to it {\sl via} web services, so it is up to you, the user,
to decide which service to use when working with nucleic acid sequences. The
-table below shows which alignment programs are most appropriate
+table shows which alignment programs are most appropriate
for nucleotide alignment. Generally, all will work, but some may be more suited
to your purposes than others. We also note that none of these include
support for taking RNA secondary structure prediction into account when aligning
\exercise{Visualizing Protein Features on Coding Regions}
{
\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.}
-\exstep{Open the {\sl DAS Settings} tab in the {\sl Sequence Feature Settings\ldots} window and fetch features for D49489 from the Uniprot reference server, and any additional servers that work with the Uniprot coordinate system.}
+\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.}
+\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,
+and any additional servers that work with the Uniprot coordinate system.}
\exstep{Mouse over the features retrieved, note that they have been mapped onto the coding regions, and in some cases broken into several parts to cover the distinct exons.}
\exstep{Open a new alignment view containing the Uniprot protein product with {\sl Calculate $\Rightarrow$ Get Cross References $\Rightarrow$ Uniprot } and examine the database references and sequence features. Experiment with the interactive highlighting of codon position for each residue.
}
\end{figure}
-\exercise{Viewing RNA Structures}{
-\label{viewingrnaex}
+\exercise{Viewing RNA Structures}
+{ \label{viewingrnaex}
-\exstep{Import RF00162 from Rfam (Full).}
+\exstep{Import RF00162 from Rfam (Full) using Fetch sequence(s) option in File
+menu.}
\exstep{Select {\sl Colour by RNA Helices} to shade the alignment by
the secondary structure annotation provided by Rfam.}
+
\exstep{Open VARNA with {\sl Structure $\Rightarrow$ View Structure
$\Rightarrow$ RNA Secondary Structure}.
+In the VARNA Structures Manager toggle between (i) secondary structure
+(alignment) (with gaps) and (ii) trimmed secondary structure (alignment).
+Explore the difference between trimmed and untrimmed views.
+Click on different residues and located them in the sequence alignment window.}
- Explore the difference between trimmed and untrimmed views for the
- structure.
-}
-\exstep{Add and link a Jmol structure view
-for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
-structure along-side the consensus structure for the alignment by adding
-reference annotation from the 3D structure.
-
-{\sl Hint: You need to make sure the RNAview service is enabled in your {\sl
-Structure} preferences to obtain RNA secondary structure annotation from PDB
-files.}}
+\exstep{In the VARNA Structures Manager, right click on display window to
+bring up the pop up context menu. Investigate option within File, Export, Display
+and Edit sections.}
-\exstep{Perform a secondary structure prediction. Enable the VIENNA consensus
-calculation via the {\sl Web Services} menu. Compare this with the annotation
-line provided by Rfam.}
+\exstep{Perform a secondary structure prediction in {\sl Web Services}. Enable
+the VIENNA consensus calculation via the {\sl Web Services} menu and select
+Change RNAAIiFold settings option.}
+% Compare this with the annotationline provided by Rfam.
\exstep{Edit the VIENNA calculation settings to show
-Base Pair probabilities.
+Base Pair probabilities. Explore how editing the alignment affects the consensus
+calculation.}
+
+\exstep{Import 2GIS from PDB database using 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.}
+%\exstep{Add and link a Jmol structure view
+%for Bacillus\_amyloliquef.9 for 3NPB (from the PDB). Display the secondary
+%structure along-side the consensus structure for the alignment by adding
+%reference annotation from the 3D structure.
+
+%{\sl Hint: You need to make sure the RNAview service is enabled in your {\sl
+%Structure} preferences to obtain RNA secondary structure annotation from PDB
+%files.}}
-Explore how editing the alignment affects the consensus
-calculation.} }
+ }
\end{document}
git://source.jalview.org / jalview-manual.git / blobdiff