From 913195128baa7d5b4c3522eabaa8f08b9103063c Mon Sep 17 00:00:00 2001 From: Suzanne Duce Date: Fri, 5 Dec 2014 17:31:13 +0000 Subject: [PATCH] 90% of chapter 1 edits for London workshop. Though I would like to test run the text and exercises more if there was more time. --- TheJalviewTutorial.tex | 70 ++++++++++++++++++++++++++++++++---------------- 1 file changed, 47 insertions(+), 23 deletions(-) diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 1a9eda5..1574b35 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -1086,9 +1086,9 @@ instead of sequences. the selection, and experiment with the `Hide all but selected region' function in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}} \exstep{Select some sequences and pick one to represent the rest by hoovering -the mouse over this sequence. Bring up the selection pop-up menu by right -clicking and then seelct {\sl (Sequence ID) $\Rightarrow$ Represent group -with (Sequence ID)}. To reveal these hidden sequences, right click on the +the mouse over this sequence. Bring up the Sequence ID pop-up menu by right +clicking and then seelct {\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 the pop-up menu select Reveal All.}} @@ -1103,13 +1103,15 @@ The alignment view provides an interactive editing interface, allowing gaps to b The Jalview alignment editing model is different to that used in other alignment editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position, editing has the effect of shifting the rest of the sequence(s) being edited down or up-stream with respect to the rest of alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment, but does not avoid the `knock-on' effect which is sometimes undesirable. However, its effect can be limited by performing the edit within a selected region. In this case, gaps will only be removed or inserted within the selected region. Edits are similarly constrained when they occur adjacent to a hidden column. -\subsubsection{Introducing gaps in a single sequence} +\subsubsection{Introducing Gaps in a Single equence} -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 till the required number of gaps has been inserted. +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 untill 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} +\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. @@ -1123,7 +1125,7 @@ right (respectively). Slides occur regardless of the region selection - which, for example, allows you to easily reposition misaligned subfamilies within a larger alignment. -\subsubsection{Undoing edits} +\subsubsection{Undoing Edits} Jalview supports the undoing of edits {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit} alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the @@ -1134,7 +1136,7 @@ annotation cannot be undone. % % better idea to introduce hiding sequences, and use the invert selection, hide % others, to simplify manual alignment construction -\exercise{Editing alignments}{ +\exercise{Editing Alignments}{ \label{mousealedit} % TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF {You are going to manually reconstruct part of the example Jalview alignment @@ -1161,15 +1163,20 @@ Sequences}). } the left so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.} \exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and -O80429\_MAIZE (Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then +O80429\_MAIZE + +(Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then deselect FER1\_MAIZE), and use the $\Rightarrow$ key to slide them to so they begin at column 5 of the alignment view.} \exstep{ Select all the visible -sequences in the block by pressing [CTRL]-A. Insert a single gap in all selected -sequences at column 38 by holding [CTRL] and clicking on the R in FER1\_SPIOL and -dragging one column to right. Insert another gap at column 47 in all sequences in -the same way.} +sequences (those not hidden) in the block by pressing [CTRL]-A. + +Insert a single +gap in all selected sequences at column 38 of the alignment by holding [CTRL] +and clicking on the R at column 38 in the FER1\_SPIOL, then drag one +column to right. +Insert another gap at column 47 in all sequences in the same way.} \exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by inserting two additional gaps after the gap at column 47: First press [ESC] to @@ -1179,14 +1186,16 @@ two columns to the right.} \exstep{ Now complete the alignment of FER1\_SPIOL with a {\bf locked edit} by pressing [ESC] and select columns 47 to 57 of the FER1\_SPIOL row. Move the mouse onto the G at column 50, -hold [SHIFT] and drag the G to the left by one column to insert a gap at column -57.} +hold [SHIFT] and drag the G in column 47 of FER1\_SPIOL to the left by one +column to insert a gap at column 57.} \exstep{ In the next two steps you will complete the alignment of the last two sequences. Select the last two sequences (FER1\_MAIZE and O80429\_MAIZE), then press [SHIFT] and click and drag the initial methionine of O80429\_MAIZE 5 columns to the right -so it lies at column 10. Keep holding [SHIFT] and click and drag to insert +so it lies at column 10. + +Keep holding [SHIFT] and click and drag to insert another gap at the proline at column 25 (25C in cursor mode). Remove the gap at column 44, and insert 4 gaps at column 47 (after AAPM).} @@ -1242,7 +1251,7 @@ together). Note that the deletion will only occur if the gaps are in the same columns in all sequences in the selected group, and those columns are to the right of the selected residue. -\exercise{Keyboard edits}{ \item{This continues on from exercise +\exercise{Keyboard Edits}{ \item{This continues on from exercise \ref{mousealedit}, and recreates the final part of the example ferredoxin alignment from the unaligned sequences using Jalview's keyboard editing mode. @@ -1260,8 +1269,9 @@ Now, enter cursor mode by pressing [F2]} % TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783 \exstep{Insert 58 gaps at the start of the first sequence (FER\_CAPAA). Press {\sl 58} then {\sl [SPACE]}. } \exstep{Go down one sequence and select rows 2-5 as a block. Click on the second sequence ID (FER\_CAPAN). Hold down shift and click on the fifth (FER1\_PEA). } -\exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing {\sl 1,2} then pressing {\sl [RETURN]}. Now insert 6 gaps. Type {\sl 6} then hold down {\sl [CTRL]} and press {\sl [SPACE]}.} -\exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47. +\exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing +{\sl 1,2} then press {\sl [RETURN]}. Now insert 6 gaps in all the sequences. +Type {\sl 6} then hold down {\sl [CTRL]} and press {\sl [SPACE]}.} \exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47. Press {\sl 34C} then {\sl [CTRL]-[SPACE]}. Press {\sl 38C} then [CTRL]-[SPACE]. Press {\sl 47C} then {\sl 3 [CTRL-SPACE]} the first through fourth sequences are now aligned.} @@ -1282,7 +1292,10 @@ appears to happen, it may be that you have sequence feature annotation displayed, and you may have to disable it using the {\sl View $\Rightarrow$ Show Features} option before you can see your colourscheme. -There are two main types of colouring styles: simple static residue colourschemes and dynamic schemes which use conservation and consensus analysis to control colouring. A hybrid colouring is also possible, where static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below. +There are two main types of colouring styles: {\bfsimple static residue} +colourschemes and {\bfdynamic schemes} which use conservation and consensus +analysis to control colouring. A {\bfhybrid colouring} is also possible, where +static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below. \subsection{Colouring the Whole Alignment} @@ -1296,9 +1309,16 @@ There are two main types of colouring styles: simple static residue colourscheme \subsection{Colouring a Group or Selection} -Selections or groups can be coloured in two ways. The first is {\sl via} the Alignment Window's {\sl Colour} menu as stated above, after first ensuring that the {\sl Apply Colour To All Groups} flag is not selected. This must be turned {\sl off} specifically as it is {\sl on} by default. When unticked, selections from the Colours menu will only change the colour for residues in the current selection, or the alignment view's ''background colourscheme'' when no selection exists. +Selections or groups can be coloured in two ways. The first is {\sl via} the Alignment Window's {\sl Colour} menu as stated above, + after first ensuring that the {\sl Apply Colour To All Groups} flag is not selected. + This must be turned {\sl off} specifically as it is {\sl on} by default. + When unticked, selections from the Colours menu will only change the colour for residues in the current selection, + or the alignment view's ``background colourscheme'' when no selection exists. -The second method is to use the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour} context menu option obtained by right clicking on the group (Figure \ref{colgrp}). This only changes the colour of the current selection or group. +The second method is to select sequences and right click mouse to open pop-up +menu and seelct {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group +Colour} from context menu options +(Figure \ref{colgrp}). This only changes the colour of the current selection or group. \begin{figure}[htbp] \begin{center} @@ -1470,8 +1490,12 @@ secondary structure row is present on the alignment. \includegraphics[width=2.75in]{images/col_rnahelix.pdf} } \exercise{Colouring Alignments}{ +\exstep{Ensuring that the {\sl Apply Colour To All Groups} flag is not selected +in View sequence alignment menu. + This must be turned {\sl off} specifically as it is {\sl on} by default.} \exstep{ -Open a sequence alignment, for example the PFAM domain PF03460. Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. 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. +Open a sequence alignment, for example the PFAM domain PF03460 in PFAM seed. +Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. 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}. Select a group of around 4 similar sequences. Use the context menu (right click on the group) option {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour $\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which were not coloured are now coloured. The calculations performed for dynamic colouring schemes like Blosum62 are based on the group being coloured, not the whole alignment (this also explains the colouring changes observed in exercise \ref{exselectgrpcolour} during the group selection step). -- 1.7.10.2