\exstep{Return to the alignment window. Look at the status bar (lower left hand
corner of the alignment window) as you move the mouse over the alignment. It indicates information about the
sequence and residue under the cursor.}
-\exstep{Press [F2] to enter {\bf Cursor mode}. Use the direction {\bfarrow
-keys} to move the cursor around the alignment.}
+\exstep{Press [F2] key (or [Fn]/[F2] on Mac) to enter {\bf Cursor mode}. Use
+the direction {\bfarrow keys} to move the cursor around the alignment.}
\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
two different positions if gaps are inserted into the sequence. Move to sequence 5,
Select the {\bf PFAM seed} database and click ok, then enter the accession
number {\bf PF03460} and click OK. An alignment of about 174 sequences should
-load.
+load, these can be viewed using the Overview window accessible from {\sl View
+$\Rightarrow$ Overview Window $\Rightarrow$ From File}.
Several database IDs
or accession numbers can be loaded by using semicolons to separate them.}}
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
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{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
+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
+the right-hand edge of the selected group.}
\exstep{The current selection can be {\bf exported} and saved by right clicking
on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an
\subsubsection{Introducing Gaps in a Single Sequence}
-To introduce a gap, place the cursor on the residue to the immediate right of
-where the gap should appear. Hold down the SHIFT key and the left mouse button,
-then drag the sequence to the right until the required number of gaps has been inserted.
+To introduce a gap, first select the sequence in the sequence ID panel and
+then place the cursor on the residue to the immediate right of where the gap
+should appear. Hold down the SHIFT key and the left mouse button, then drag the sequence to the right until the required number of gaps has been inserted.
One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long. Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
\subsubsection{Introducing Gaps in all Sequences of a Group}
-To insert gaps in all sequences in a selection or group, place the mouse cursor on any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the CTRL key and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
+To insert gaps in all sequences in a selection or group, select the
+required sequences in the sequence ID panel and then place the mouse cursor on
+any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the CTRL key and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
Gaps can be removed by dragging the residue to the immediate right of the gap
leftwards whilst holding down [SHIFT] (for single sequences) or [CTRL] (for a group of sequences).
\subsubsection{Sliding Sequences}
Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more
-sequences are selected will ``slide'' the selected sequences to the left or
-right (respectively). Slides occur regardless of the region selection -
+sequences are selected will ``slide'' the entire selected sequences to the left
+or right (respectively). Slides occur regardless of the region selection -
which, for example, allows you to easily reposition misaligned subfamilies
within a larger alignment.
Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu.
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 selecting {\sl View $\Rightarrow$ 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
+\exstep{Hide all the annotation rows by selecting {\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
annotation row labels to bring up the pop-up context menu, then select {\sl
Hide This Row}. Bring up the pop-up context menu again and select {\sl
Show All Hidden Rows} to reveal them.}
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