From d206ac2463e081918f458a2a82537d8939dbe560 Mon Sep 17 00:00:00 2001 From: Suzanne Duce Date: Thu, 30 Apr 2015 16:53:54 +0000 Subject: [PATCH] thursday edits to manual --- TheJalviewTutorial.tex | 134 ++++++++++++++++++++++++++++++++---------------- 1 file changed, 90 insertions(+), 44 deletions(-) diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 6f21d1f..d77f4d4 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -79,7 +79,7 @@ Jalview 2.8.2 \vspace{0.5in} {\huge -Manual and Introductory Tutorial } +Manual and Introductory Tutorial } \vspace{2.4in} @@ -1925,7 +1925,7 @@ when associated alignment views are modified. \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 @@ -1940,8 +1940,9 @@ $\Rightarrow$ 1A70}. A structure viewing window appears. Rotate the molecule by \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.} } @@ -1976,7 +1977,7 @@ parts of each molecule used to construct the superposition are rendered using 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. @@ -2024,7 +2025,8 @@ Sequence Alignment}{\label{superpositionex} \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 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. @@ -2034,13 +2036,16 @@ moved on to the other. If this doesn't happen, use the Align function in the Jmo \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 @@ -2111,10 +2116,14 @@ free memory available. {\sl Use the following webstart link: -\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}.}} -\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 offical 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 @@ -2305,7 +2314,13 @@ The {\sl View $\Rightarrow$ Associated Nodes With $\Rightarrow$ .. } submenu is \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 offical 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.} @@ -2340,10 +2355,12 @@ can help when working with larger alignments. \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. } } @@ -2362,10 +2379,15 @@ The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Re \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 Redunancy 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.} } @@ -2403,14 +2425,14 @@ G.J. (1993) {\sl CABIOS } {\bf 9}, 745-756}. 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. @@ -2419,8 +2441,8 @@ 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} @@ -2435,11 +2457,15 @@ Visual tab in the Jalview desktop's preferences dialog box. \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 sequennce 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 @@ -2734,8 +2760,8 @@ Systems Biology} {\bf 7} 539 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 @@ -2769,7 +2795,7 @@ The re-alignment option is currently only supported by ClustalW and Clustal 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. @@ -2783,18 +2809,35 @@ Finally, the results of each subjob will be concatenated with the hidden regions 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.} } @@ -3043,7 +3086,7 @@ alignment.} } \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. @@ -3184,7 +3227,10 @@ annotation panel and selecting \textbf{Show hidden annotation}. \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.} -- 1.7.10.2