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23 <title>Split Frame Views</title>
26 <p><strong>Split Frame Views</strong></p>
28 Jalview provides a special viewing mode to show Coding DNA (cDNA)
29 and protein product alignments as a split view, with cDNA above and
30 protein below. The two alignments are linked, allowing editing and
31 analysis to be performed at both the peptide and nucleotide level.
32 Linked protein alignments also have an additional
33 <strong>cDNA Consensus</strong> annotation row, showing the
34 distribution of codons at each column
35 of the protein alignment.
38 Split Frame views can be <a
39 href="#opensplit">created in a number of ways</a>. In the Jalview
40 Desktop, Split Frame views are saved in Jalview Projects, like any
43 <p><strong>Operations supported in Split Frame Mode</strong></p>
44 <p>Split Frame views allow the following:
47 <li>Mouseover or scrolling of either alignment is followed by
48 the other (unless you turn off <strong><a
49 href="../menus/alwview.html">"View→Automatic
50 Scrolling"</a></strong>)
52 <li>On selecting rows, columns or regions in one alignment, the
53 corresponding selection is made in the other</li>
54 <li>Sequence ordering in one alignment (using the cursor, or <strong><a
55 href="../calculate/sorting.html">"Calculate→Sort")</a></strong> is
56 also applied to the other
58 <li>Editing (gap insertion / deletion) in the protein alignment
59 is reflected in the cDNA (but not vice versa)</li>
60 <li>Any trees imported or created with <strong><a
61 href="../calculations/tree.html">"Calculate Tree"</a></strong> on one of
62 the views allow both cDNA and Protein views to be grouped,
65 <li>To allow for the different widths in cDNA and Protein
66 alignments, the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong>
67 menu option has an option 'Scale protein residues to codons'. This
68 option will make each protein residue the same width as a DNA
69 codon (so the alignments 'line up' vertically)
71 <li><strong>"View→Protein"</strong> (in the cDNA panel)
72 or <strong>"View→Nucleotide"</strong> (in the protein panel)
73 allows you to show or hide one or other of the linked alignment
75 <li>Panel heights are adjusted dragging the divider between
76 them using the mouse</li>
77 <li><a href="menus/alwview.html"><strong>"View→New
78 View / Expand Views / Gather Views"</strong></a> behave as for a normal
79 alignment window, but always create new views as Split Frames</li>
81 <p>An alignment annotation row on the protein alignment shows the <strong><a href="../calculations/consensus.html">cDNA consensus</a></strong> for each peptide column.<br/>
82 This consensus may reveal variation in nucleotides coding for conserved protein residues.</p>
84 <a name="opensplit"/><p><strong>Opening a Split Frame View</strong></p>
85 <p>A Split Frame View can be opened in one of the following ways:</p>
86 <p><strong><em>Add Sequences</em></strong></p>
87 <p>If you add (coding) DNA sequences to an open peptide alignment, or vice versa, <em>and</em> at least one DNA sequence translates to one of the
88 peptide sequences, then the option to open in a split window is offered. The DNA may include start and/or stop codons, but no non-coding (intron)
90 If more than one cDNA variant is present in the alignment, Jalview will first try to match these to protein sequences based on any retrieved cross-references, and failing that, pairwise as they are ordered in the alignments.
92 <p>This option is available in Jalview Desktop (when adding sequences by any supported method), and Jalview applet (adding from textbox).
93 The additional options below apply to Jalview Desktop only.</p>
95 <p><strong><em>Translate as cDNA</em></strong></p>
96 <p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Translate as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this option shows the DNA and its
97 calculated protein product in a Split Frame view.</p>
99 <p><strong><em>Get Cross-References</em></strong></p>
100 <p>Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Get Cross-References"</a></strong> is available for fetched sequences which have cross-references to other databases.
101 On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.</p>
103 <p><strong><em>Realign a Split View</em></strong></p>
104 <p>If you invoke a web service to realign either half of a Split
105 Frame, then the resulting realignment is displayed in a new Split
109 <li>the alignment you chose to realign (for example, peptide)
110 is displayed as aligned by the external web service</li>
111 <li>Jalview reconstructs the alignment of its complement (in
112 this case, cDNA) by inserting gaps in the corresponding positions</li>
115 <a name="reconalignment" /><strong>Reconstructed Alignments</strong>
118 Reconstructed alignments are typically <em>not</em> the same as the
119 alignment produced by aligning the complement sequence set directly
120 with the external service. However, in the case of protein
121 alignments, a reconstructed cDNA alignment is often more reliable
122 than one calculated without coding information. Reconstructed cDNA
123 alignments are also more informative than the original protein
124 alignment when calculating phylogenetic trees or performing other
125 kinds of molecular evolution analysis.
128 <em>Split Frame Views were introduced in Jalview 2.9</em>