% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-10th May 2019
+24th September 2020
\end{center}
\exstep{{\bf Loading sequences from a file:} Close all windows using the
{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser and save the fasta file (.fa) file to your desktop using {\sl File
+your web browser. Then from the brwoser, save the fasta file (.fa) file to your desktop using {\sl File
$\Rightarrow$ Save Page as}.
-Open the file you have just saved in Jalview by selecting {\sl File
+Open the file you have just saved on your computer in Jalview by selecting {\sl File
$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
Select the file and click {\sl OK} to load.}
\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
-(i) Drag the alignment.fa file that you have just saved from its folder and
+(i) Drag the alignment.fa file that you have just saved on your computer from its folder and
drop it onto the Jalview desktop window, the alignment should open.
(ii) Open
\exstep{{\bf The text editor:}
-(i) Open the alignment.fa file using text editor.
+(i) Open the alignment.fa file that you saved previously using text editor.
Copy the sequence text into the clipboard using [CTRL]-A and then [CTRL]-C.
(ii) Move the mouse pointer onto the Jalview desktop window's background and right-click
\exstep{Check this file by closing all windows and opening it with Jalview, or by
browsing to it with your web browser.}
\exstep{Repeat the previous steps saving the files in different file formats.}
+\exstep{Open the files in a normal text editor and compare the appearance of the different file formats.}
\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}.
Select and copy this alignment to the clipboard using the textbox menu options
{\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}.
Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
Press {\bf Q} to mark this position.
Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
-to complete the selection. Note to clear the selection press the [ESC]
+to complete the selection.}
+\exstep{Note to clear the selection press the [ESC]
key.}
\exstep{To create a group from the selected the region, click the
right mouse button when mouse is on the selection, this opens a
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
} menu and select {\sl Percentage Identity}.
This will turn the selected region into a group and colour it accordingly.}
-\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences in
+\exstep{Hold down [CTRL] ([CMD] on Mac) or [SHIFT] and use the mouse to select and deselect sequences in
the alignment by clicking on their Sequence ID label. Note how the group expands
to include newly selected sequences, and the Percentage Identity colouring changes. }
\exstep{ Another way to resize the group is by using the mouse to click and drag
need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$
All Sequences.}) }
\exstep{
-Repeat the process but use a non-contiguous set of sequences. Note that when
+Repeat the process but use a non-contiguous set of sequences using the [CTRL] ([CMD] on Mac) key. Note that when
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.}
\exstep{Select a region of the alignment, and experiment with the {\sl Hide all
-but selected region} option in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
+but selected region} option. In the alignment window menu, {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
but selected region.}} \exstep{Select some sequences, pick one to represent the rest by hovering
the mouse over this sequence. Bring up the Sequence ID context menu by right
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
right of the selected residue.
-\exercise{Editing Alignments}
+\exercise{Editing Alignments Homework Exercise}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
{
}
-\exercise{Keyboard Edits}
+\exercise{Keyboard Edits Homework Exercise}
{
\label{keyboardsex}
This continues on from the previous exercise, and recreates the final part of the example ferredoxin
\exercise{Colouring Alignments}{
\label{color}
Note: Ensure that the {\sl Apply Colour
-To All Groups} flag is not selected in {\sl Colour} menu in the alignment window.
+To All Groups} flag is not selected (ie unticked) 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.
Clustalx} and note the colour change. Now try all the other colour schemes in the {\sl Colour} menu.
Note that some colour schemes do not colour all residues.}
\exstep{Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62 score}. Select a group
-of around 4 similar sequences. Use the context menu (right click on the group)
+of around 4 similar sequences. Use the context menu (right click on the residues in the group)
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62 score} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
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
+Note: Feature colours overlay residue colouring and this may mask residue colouring. If this is an issue, he 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}.}
Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
sequence ID format and so on. }
\exstep{Hide all the annotation rows by toggling {\sl Annotations $\Rightarrow$
-Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.} \exstep{Deselect {\sl Format $\Rightarrow$ Wrap}. Right click on the
+Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.}
+\exstep{Deselect {\sl Format $\Rightarrow$ Wrap}.}
+\exstep{Right click on the
annotation row labels to bring up the context menu, then select {\sl
Hide This Row}. Bring up the context menu again and select {\sl
Show All Hidden Rows} to reveal them.}
dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}.
The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot}.}
\exstep{Move the mouse to the top left hand corner of the annotation labels -
-a up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed
+a up/down arrow symbol should appear - click on the icon, the height of the {\sl Annotation Area} can be changed
by clicking and dragging this icon up or down.}
\bf See the video at:
\url{http://www.jalview.org/training/Training-Videos}.}
Enter a suitable Sequence Feature Name (e.g. ``Iron binding site") in the
appropriate box. Click on the Feature Colour bar to change the colour if
desired, add a short description (``One of four Iron binding Cysteines") and
-press {\sl OK}. The features will then appear on the sequences. } \exstep{Roll
+press {\sl OK}. The features will then appear on the sequences. }
+ \exstep{Roll
the mouse cursor over the new features.
Note that the position given in the tool tip is the residue number, not the column number.
-To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC],
- then insert a gap in sequence 3 at column 95 using the [SHIFT] key.
-Roll the mouse over the features and you will see that the feature has moved
+To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC]. Select the [SHIFT] key,
+ then insert a gap in sequence 3 at column 95 by moving the mouse.
+Roll the mouse cursor over the features and you will see that the feature has moved
with the sequence. Delete the gap you created using {\sl Edit
$\Rightarrow$ Undo}.
}
\exstep{Select the last three sequences in the MAFFT alignment (you may need the scroll down the alignment), and de-align them
with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect these
sequences. Then submit this view for re-alignment with {\sl ClustalO}.}
-\exstep{Return to the alignment window in section (c), use [CTRL]-Z (undo) to
+\exstep{Return to the MAFFT alignment window in section (c), use [CTRL]-Z (undo) to
recover the alignment of the last three sequences in this MAFFT alignment.
Once the ClustalO re-alignment has completed, compare the results of
re-alignment of the three sequences with their alignment in the original MAFFT result.}
and dragging it up to the top of the annotations.}
\exstep{In the column alignment ruler, select a column exhibiting with about 50\%
of its residues conserved ({\em ie. about 50\% in the consensus histogram})
- that lies within the central conserved region of the alignment.
-(Column 74 is used in \href{https://youtu.be/m-PjynicXRg}{the Tree video}).}
+ that lies within the central conserved region of the alignment.}
\exstep{Subdivide the alignment
according to this selection using {\sl Select $\Rightarrow$ Make Groups for Selection}.}
\exstep{Re-order the alignment according to the new groups that have been
\exstep{Select the FER1\_MAIZE sequence (near bottom of the alignment). Right-click the ID label to open the context menu,
select {\sl $\Rightarrow$ 3D Structure Data}.}
-\exstep{This opens the Structure Chooser dialog, pick 1gaq from the list.
+\exstep{This opens the Structure Chooser dialog, pick 1gaq or 3b2f from the list.
Make sure the {\sl Superpose} option is checked before clicking the {\bf Add}
button. This superimpose the structure associated with
FER1\_MAIZE with the one associated with FER1\_SPIOL.
git://source.jalview.org / jalview-manual.git / blobdiff