3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>Split Frame Views</title>
27 <strong>Split Frame Views</strong>
30 Jalview provides a special viewing mode to show Coding DNA (cDNA)
31 and protein product alignments as a split view, with cDNA above and
32 protein below. The two alignments are linked, allowing editing and
33 analysis to be performed at both the peptide and nucleotide level.
34 Linked protein alignments also have an additional <strong>cDNA
35 Consensus</strong> annotation row, showing the distribution of codons at
36 each column of the protein alignment.
39 Split Frame views can be <a href="#opensplit">created in a
40 number of ways</a>. In the Jalview Desktop, Split Frame views are
41 saved in Jalview Projects, like any other alignment view.
43 <p><strong><a name="virtualfeats">Virtual Sequence Features</a></strong>
45 <p>Since Jalview 2.11.1, sequence features displayed in either CDS
46 or Protein can be shown as 'Virtual Features' mapped onto the other
47 view. Features describing non-synonymous genomic sequence variation
48 in coding regions are dynamically translated when shown in the
50 <p>The display of virtual features and whether they are rendered
51 below or above features local to the aligned sequences is controlled
52 by a check box shown in the view's Sequence Feature Settings dialog
53 box. For convenience, Protein and CDS feature settings for a linked
54 CDS/Protein view are shown as tabs in a single dialog box, allowing
55 easy access to display and filter settings for each view.</p>
57 <img width="631" align="center"
58 alt="Linked CDS and Protein Feature Settings showing Virtual Feature checkbox"
59 src="linkedfeatsettings.png" /> <em>CDS and Protein feature
60 settings tabs and corresponding views showing 'Virtual Features'
61 from each view overlaid on the other (created with Jalview 2.11.1.0).</em>
64 When virtual features are enabled, they are also shown on any linked
65 3D structure views when 'Colour by Sequence' is enabled, and
66 exported as GFF and Jalview Features files (mapped to their
67 associated virtual coordinates). Both the original and the mapped
68 locations are also included in <a href="seqfeaturereport.html">Sequence
72 <strong>Operations supported in Split Frame Mode</strong>
74 <p>Split Frame views allow the following:
76 <li>Mouseover or scrolling of either alignment is followed by
77 the other (unless you turn off <strong><a
78 href="../menus/alwview.html">"View→Automatic
79 Scrolling"</a></strong>)
81 <li>On selecting rows, columns or regions in one alignment, the
82 corresponding selection is made in the other</li>
83 <li>Sequence ordering in one alignment (using the cursor, or <strong><a
84 href="../calculations/sorting.html">"Calculate→Sort")</a></strong>
85 is also applied to the other
87 <li>Editing (gap insertion / deletion) in the protein alignment
88 is reflected in the cDNA (but not vice versa)</li>
89 <li>Any trees imported or created with <strong><a
90 href="../calculations/tree.html">"Calculate Tree"</a></strong> on
91 one of the views allow both cDNA and Protein views to be grouped,
94 <li>To allow for the different widths in cDNA and Protein
95 alignments, the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong>
96 menu option has an option 'Scale protein residues to codons'. This
97 option will make each protein residue the same width as a DNA
98 codon (so the alignments 'line up' vertically).</li>
99 <li><a name="mirror" />The 'Use same font for cDNA and peptide'
100 checkbox, when enabled, ensures that font or font-size changes in
101 either the cDNA or Protein alignment will also be mirrored. (<em>Added
103 <li><strong>"View→Protein"</strong> (in the cDNA panel)
104 or <strong>"View→Nucleotide"</strong> (in the protein panel)
105 allows you to show or hide one or other of the linked alignment
107 <li>Panel heights are adjusted by dragging the divider between
108 them using the mouse</li>
109 <li><a href="../menus/alwview.html"><strong>"View→New
110 View / Expand Views / Gather Views"</strong></a> behave as for a normal
111 alignment window, but always create new views as Split Frames</li>
114 An alignment annotation row on the protein alignment shows the <strong><a
115 href="../calculations/consensus.html">cDNA consensus</a></strong> for
116 each peptide column.<br /> This consensus may reveal variation in
117 nucleotides coding for conserved protein residues.
120 <a name="opensplit" />
122 <strong>Opening a Split Frame View</strong>
124 <p>A Split Frame View can be opened in one of the following ways:</p>
126 <strong><em>Add Sequences</em></strong>
129 If you add (coding) DNA sequences to an open peptide alignment, or
130 vice versa, <em>and</em> at least one DNA sequence translates to one
131 of the peptide sequences, then the option to open in a split window
132 is offered. The DNA may include start and/or stop codons, but no
133 non-coding (intron) sequence.<br> If more than one cDNA variant
134 is present in the alignment, Jalview will first try to match these
135 to protein sequences based on any retrieved cross-references, and
136 failing that, pairwise as they are ordered in the alignments.
137 <p>This option is available in Jalview Desktop (when adding
138 sequences by any supported method), and Jalview applet (adding from
139 textbox). The additional options below apply to Jalview Desktop
143 <strong><em>Translate as cDNA</em></strong>
146 Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Translate
147 as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this
148 option shows the DNA and its calculated protein product in a Split
153 <strong><em>Get Cross-References</em></strong>
156 Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Get
157 Cross-References"</a></strong> is available for fetched sequences which have
158 cross-references to other databases. On selecting protein
159 cross-references (for a cDNA alignment), or DNA xrefs (for peptide),
160 a Split Frame view is opened showing cDNA and peptide.
164 <strong><em>Realign a Split View</em></strong>
166 <p>If you invoke a web service to realign either half of a Split
167 Frame, then the resulting realignment is displayed in a new Split
170 <li>the alignment you chose to realign (for example, peptide)
171 is displayed as aligned by the external web service</li>
172 <li>Jalview reconstructs the alignment of its complement (in
173 this case, cDNA) by inserting gaps in the corresponding positions</li>
176 <a name="reconalignment" /><strong>Reconstructed
180 Reconstructed alignments are typically <em>not</em> the same as the
181 alignment produced by aligning the complement sequence set directly
182 with the external service. However, in the case of protein
183 alignments, a reconstructed cDNA alignment is often more reliable
184 than one calculated without coding information. Reconstructed cDNA
185 alignments are also more informative than the original protein
186 alignment when calculating phylogenetic trees or performing other
187 kinds of molecular evolution analysis.
190 <em>Split Frame Views were introduced in Jalview 2.9</em>