2 <head><title>Alignment Window Menus</title></head>
\r
5 <p><strong>Alignment Window Menus</strong></p>
\r
7 <li><strong>File</strong>
\r
9 <li><strong>Fetch Sequence</strong><br>
\r
10 <em>Shows a dialog window in which you can select known ids from Uniprot,
\r
11 EMBL, EMBLCDS or PDB database using Web Services provided by the European
\r
12 Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence
\r
13 Fetcher</a></em>.</li>
\r
14 <li><strong>Save As<br>
\r
15 </strong><em>Save the alignment to local file. A file selection window
\r
16 will open, use the "Files of type:" selection box to determine
\r
17 which <a href="../io/index.html">alignment format</a> to save as.</em></li>
\r
18 <li><strong>Export</strong> <em><br>
\r
19 Creates an alignment graphic with the current annotation, alignment background
\r
20 colours and group colours. If the alignment is <a
\r
21 href="../features/wrap.html">wrapped</a>, the output will also be wrapped
\r
22 and will have the same visible residue width as the open alignment. </em>
\r
24 <li><strong>HTML<br>
\r
25 </strong><em>Create a <a href="../io/index.html#export">web page</a>
\r
26 from your alignment.</em></li>
\r
28 </strong><em>Create an <a href="../io/index.html#export">Encapsulated
\r
29 Postscript</a> file from your alignment.</em></li>
\r
31 </strong><em>Create a <a href="../io/index.html#export">Portable Network
\r
32 Graphics</a> file from your alignment.</em></li>
\r
35 <li><strong>Output to Textbox<br>
\r
36 </strong><em>The alignment will be displayed in plain text in a new window
\r
37 which you can "Copy and Paste" using the pull down menu, or
\r
38 your standard operating system copy and paste keys. <br>
\r
39 Select the format of the text by selecting one of the following menu items.</em>
\r
41 <li><strong>FASTA</strong> <em></em></li>
\r
42 <li><strong>MSF</strong></li>
\r
43 <li><strong>CLUSTAL</strong></li>
\r
44 <li><strong>BLC</strong></li>
\r
45 <li><strong>PIR</strong></li>
\r
46 <li><strong>PFAM</strong></li>
\r
49 <li><strong>Print<br>
\r
50 </strong><em>Jalview will print the alignment using the current fonts
\r
51 and colours of your alignment. If the alignment has annotations visible,
\r
52 these will be printed below the alignment. If the alignment is wrapped
\r
53 the number of residues per line of your alignment will depend on the paper
\r
54 width or your alignment window width, whichever is the smaller. </em></li>
\r
55 <li><strong>Load Associated Tree<br>
\r
56 </strong><em>Jalview can <a
\r
57 href="../calculations/treeviewer.html">view trees</a> stored in the Newick
\r
58 file format, and associate them with the alignment. Note: the ids of the
\r
59 tree file and your alignment MUST be the same.</em></li>
\r
60 <li><strong>Load Features / Annotations<br>
\r
61 </strong><em>Jalview load precalculated <a href="../features/featuresFormat.html">sequence
\r
62 features</a> or <a href="../features/annotationsFormat.html">alignment
\r
63 annotations</a>.</em></li>
\r
64 <li><strong>Close<br>
\r
65 </strong><em>Close the alignment window. Make sure you have saved your
\r
66 alignment before you close - either as a Jalview project or by using the
\r
67 <strong>Save As</strong> menu.<br>
\r
71 <li><strong>Edit</strong>
\r
73 <li><strong>Undo</strong><em><br>
\r
74 This will undo any edits you make to the alignment. This applies to insertion
\r
75 or deletion of gaps, cutting residues or sequences from the alignment
\r
76 or pasting sequences to the current alignment or sorting the alignment.
\r
77 <strong>NOTE:</strong> It DOES NOT undo colour changes, adjustments to
\r
78 group sizes, or changes to the annotation panel. </em></li>
\r
79 <li><strong>Redo<br>
\r
80 </strong><em>Any actions which you undo can be redone using redo. </em></li>
\r
82 </strong><em>This will make a copy of the currently selected residues
\r
83 before removing them from your alignment. Click on a sequence name if
\r
84 you wish to select a whole sequence. <br>
\r
85 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
\r
86 <li><strong>Copy</strong><br>
\r
87 <em>Copies the currently selected residues to the system clipboard - you
\r
88 can also do this by pressing <CTRL> and C (<APPLE> and C on
\r
90 If you try to paste the clipboard contents to a text editor, you will
\r
91 see the format of the copied residues FASTA.</em></li>
\r
92 <li><strong>Paste </strong>
\r
94 <li><strong>To New Alignment<br>
\r
95 </strong><em>A new alignment window will be created from sequences
\r
96 previously copied or cut to the system clipboard. <br>
\r
97 Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>
\r
98 <li><strong>Add To This Alignment<br>
\r
99 </strong><em>Copied sequences from another alignment window can be
\r
100 added to the current Jalview alignment. </em></li>
\r
103 <li><strong>Delete<br>
\r
104 </strong><em>This will delete the currently selected residues without
\r
105 copying them to the clipboard. Like the other edit operations, this can
\r
106 be undone with <strong>Undo</strong>.</em></li>
\r
107 <li><strong>Select All<br>
\r
108 </strong><em>Selects all the sequences and residues in the alignment.
\r
110 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>
\r
111 <li><strong>Deselect All<br>
\r
112 </strong><em>Removes the current selection box (red dashed box) from the
\r
113 alignment window. All selected sequences, residues and marked columns
\r
114 will be deselected. </em><em> <br>
\r
115 Use <ESCAPE> to deselect all.</em></li>
\r
116 <li><strong>Invert Selection<br>
\r
117 </strong><em>Any sequence ids currently not selected will replace the
\r
118 current selection. </em></li>
\r
119 <li><strong>Undefine Groups<br>
\r
120 </strong><em>The alignment will be reset with no defined groups.<br>
\r
121 <strong>WARNING</strong>: This cannot be undone.</em></li>
\r
122 <li><strong>Remove Left<br>
\r
123 </strong><em>If the alignment has marked columns, the alignment will be
\r
124 trimmed to the left of the leftmost marked column. To mark a column, mouse
\r
125 click the scale bar above the alignment. Click again to unmark a column,
\r
126 or select "Deselect All" to deselect all columns.</em></li>
\r
127 <li><strong>Remove Right<br>
\r
128 </strong><em>If the alignment has marked columns, the alignment will be
\r
129 trimmed to the left of the leftmost marked column. To mark a column, mouse
\r
130 click the scale bar above the alignment. Click again to unmark a column,
\r
131 or select "Deselect All" to deselect all columns.</em></li>
\r
132 <li><strong>Remove Empty Columns<br>
\r
133 </strong><em>All columns which only contain gap characters ("-",
\r
134 ".") will be deleted.<br>
\r
135 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
\r
137 <li><strong>Remove All Gaps</strong><br>
\r
138 <em>Gap characters ("-", ".") will be deleted from
\r
139 the selected area of the alignment. If no selection is made, ALL the gaps
\r
140 in the alignment will be removed.<br>
\r
141 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
\r
143 <li><strong>Remove Redundancy<br>
\r
144 </strong><em>Selecting this option brings up a window asking you to select
\r
145 a threshold. If the percentage identity between any two sequences (under
\r
146 the current alignment) exceeds this value then one of the sequences (the
\r
147 shorter) is discarded. Press the "Apply" button to remove redundant
\r
148 sequences. The "Undo" button will undo the last redundancy deletion.</em></li>
\r
149 <li><strong>Pad Gaps<br>
\r
150 </strong><em>Adds gaps to the end of all the sequences so they are all
\r
151 the same length. This is useful for making a tree using unaligned sequences.<br>
\r
152 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
\r
157 <li><strong>Search</strong>
\r
159 <li><strong>Find<br>
\r
160 </strong><em>Select this to <a href="../features/search.html">search</a>
\r
161 for residues, sequence name or residue position within the alignment.
\r
166 <li><strong>View</strong>
\r
168 <li><strong>Font<br>
\r
169 </strong><em>Change the font of the display from the "Choose Font"
\r
170 dialog box, which is shown when this item is selected. </em></li>
\r
171 <li><strong>Wrap<br>
\r
172 </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>"
\r
173 to the width of the alignment window. This is useful if your alignment
\r
174 has only a few sequences to view its full width at once.<br>
\r
175 Options are available to show the residue numbering at the start and/or
\r
176 end of an alignment as well as showing the alignment position above each
\r
178 <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot
\r
179 be edited or have regions selected on it. </em></li>
\r
180 <li><strong>Show Full Sequence ID<br>
\r
181 </strong><em>If this box is selected the sequence name will have the start
\r
182 and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
\r
183 <li><strong>Boxes</strong><em><br>
\r
184 If this is selected the background of a residue will be coloured using
\r
185 the selected background colour. Useful if used in conjunction with "Colour
\r
186 Text." </em></li>
\r
187 <li><strong>Text<br>
\r
188 </strong><em>If this is selected the residues will be displayed using
\r
189 the standard 1 character amino acid alphabet.</em></li>
\r
190 <li><strong>Colour Text<br>
\r
191 </strong><em>If this is selected the residues will be coloured according
\r
192 to the background colour associated with that residue. The colour is slightly
\r
193 darker than background so the amino acid symbol remains visible. </em></li>
\r
194 <li><strong>Show Gaps<br>
\r
195 </strong><em>When this is selected, gap characters will be displayed as
\r
196 "." or "-". If unselected, then gap characters will
\r
197 appear as blank spaces. <br>
\r
198 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</em></li>
\r
199 <li><strong>Show Annotations<br>
\r
200 </strong><em>If this is selected the "Annotation Panel" will
\r
201 be displayed below the alignment. The default setting is to display the
\r
202 conservation calculation, quality calculation and consensus values as
\r
203 bar charts. </em></li>
\r
204 <li><strong>Sequence Features<br>
\r
205 </strong><em>If the sequence names are Swissprot entries Jalview will
\r
206 use the names to retrieve <a href="../features/seqfeatures.html">sequence
\r
207 features</a> from the EBI. Features which are 1 residue in length are
\r
208 coloured red, sequences longer than 1 residue are coloured blue. Move
\r
209 the mouse over a coloured feature to display the details of the feature.
\r
211 Note: The retrieved information will update the sequence start and end
\r
212 labels if they are incorrect. </em></li>
\r
213 <li><strong>Seqence Settings </strong><br>
\r
214 <em>If features have been added to the alignment then the priority of
\r
215 rendering the features can be altered so that overlapping features can
\r
216 be displayed or hidden. See <a href="features/seqfeatures.html">Sequence
\r
217 Features</a>.</em></li>
\r
218 <li><strong><a href="../features/overview.html">Overview Window</a><br>
\r
219 </strong><em>A scaled version of the alignment will be displayed in a
\r
220 small window. A red box will indicate the currently visible area of the
\r
221 alignment. Move the visible region using the mouse. </em><strong> </strong></li>
\r
224 <li><strong>Colour</strong>
\r
226 <li><strong>Apply Colour To All Groups<br>
\r
227 </strong><em>If this is selected, any changes made to the background colour
\r
228 will be applied to all currently defined groups.</em></li>
\r
229 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
\r
230 Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
\r
231 Turn Propensity, Buried Index, Nucleotide, User Defined<br>
\r
232 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
\r
233 a description of all colour schemes.</em></li>
\r
234 <li><strong>By Conservation<br>
\r
235 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
\r
236 by Conservation</a>.</em></li>
\r
237 <li><strong>Modify Conservation Threshold<br>
\r
238 </strong><em>Use this to display the conservation threshold slider window.
\r
239 Useful if the window has been closed, or if the 'by conservation' option
\r
240 appears to be doing nothing!</em></li>
\r
241 <li><strong>Above Identity Threshold<br>
\r
242 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
\r
243 Identity</a></em><strong>.</strong></li>
\r
244 <li><strong>Modify Identity Threshold<br>
\r
245 </strong><em>Use this to set the threshold value for colouring above Identity.
\r
246 Useful if the window has been closed. <br>
\r
250 <li><strong>Calculate</strong>
\r
254 <li><strong>by ID</strong><em><br>
\r
255 This will sort the sequences according to sequence name. If the sort
\r
256 is repeated, the order of the sorted sequences will be inverted. </em></li>
\r
257 <li><strong>by Group</strong><strong><br>
\r
258 </strong><em>This will sort the sequences according to sequence name.
\r
259 If the sort is repeated, the order of the sorted sequences will be
\r
260 inverted. </em><strong></strong></li>
\r
261 <li><strong>by Pairwise Identity<br>
\r
262 </strong><em>This will sort the selected sequences by their percentage
\r
263 identity to the consensus sequence. The most similar sequence is put
\r
264 at the top. </em></li>
\r
265 <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will
\r
266 have some additional options if you have just done a multiple alignment
\r
267 calculation, or opened a tree viewer window.</em></li>
\r
270 <li><strong>Calculate Tree </strong> <br>
\r
271 <em>Functions for calculating trees on the alignment or the currently
\r
272 selected region. See <a
\r
273 href="../calculations/tree.html">calculating trees</a>.</em>
\r
275 <li><strong>Average Distance Using % Identity</strong></li>
\r
276 <li><strong>Neighbour Joining Using % Identity</strong></li>
\r
277 <li><strong>Average Distance Using Blosum62</strong></li>
\r
278 <li><strong>Neighbour Joining Using Blosum62</strong></li>
\r
281 <li><strong>Pairwise Alignments</strong><br>
\r
282 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
\r
283 alignments</a>.</em></li>
\r
284 <li><strong>Principal Component Analysis</strong><br>
\r
285 <em>Shows a spatial clustering of the sequences based on the BLOSUM62
\r
286 scores in the alignment. See <a href="../calculations/pca.html">Principal
\r
287 Component Analysis</a>.</em> </li>
\r
288 <li><strong>Translate cDNA</strong><br>
\r
289 <em>If you are viewing a cDNA alignment a very simple translation service
\r
290 is available. The translation ignores all gaps in the cDNA sequences.
\r
295 <li><strong>Web Service<br>
\r
296 </strong> <em>Selecting one of the following menu items starts a remote service
\r
297 on compute facilities at the University of Dundee. You need a continuous network
\r
298 connection in order to use these services through Jalview. </em>
\r
300 <li><strong>Alignment </strong>
\r
302 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
\r
303 <em> Submits all, or just the currently selected sequences for alignment
\r
304 with clustal W.</em></li>
\r
305 <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
\r
306 <em> Submits the alignment or currently selected region for re-alignment
\r
307 with clustal W. Use this if you have added some new sequences to an
\r
308 existing alignment.</em></li>
\r
309 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
\r
310 <em> Submits all, or jut the currently selected sequences for alignment
\r
311 using Muscle. Do not use this if you are working with nucleic acid
\r
312 sequences.</em></li>
\r
315 <li><strong>Secondary Structure Prediction</strong>
\r
317 <li><strong>JPred Secondary Structure Prediction</strong><br>
\r
318 <em>Secondary structure prediction by network consensus. The behaviour
\r
319 of this calculation depends on the current selection: </em></li>
\r
320 <li><em>If nothing is selected, and the displayed sequences appear to
\r
321 be aligned, then a JNet prediction will be run for the first sequence
\r
322 in the alignment, using the current alignment. Otherwise the first
\r
323 sequence will be submitted for prediction. </em></li>
\r
324 <li><em>If just one sequence (or a region on one sequence) has been
\r
325 selected, it will be submitted to the automatic JNet prediction server
\r
326 for homolog detection and prediction. </em></li>
\r
327 <li><em>If a set of sequences are selected, and they appear to be aligned,
\r
328 then the alignment will be used for a Jnet prediction on the <strong>first</strong>
\r
329 sequence selected in the set (that is, the one that was first clicked
\r