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]
\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 one of the the PDB file associated with
+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
{\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 offical build'' row in the table, go to the
+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
\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 offical build'' row in the table, go to the
+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}.
\exstep{Re-use or recreate the alignment and tree which you worked with in the
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 Redunancy to open the Redundancy
+\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{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 sequennce alignment window. Then display of sequence
+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.}
\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
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 / commitdiff