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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.
44 <strong>Operations supported in Split Frame Mode</strong>
46 <p>Split Frame views allow the following:
48 <li>Mouseover or scrolling of either alignment is followed by
49 the other (unless you turn off <strong><a
50 href="../menus/alwview.html">"View→Automatic
51 Scrolling"</a></strong>)
53 <li>On selecting rows, columns or regions in one alignment, the
54 corresponding selection is made in the other</li>
55 <li>Sequence ordering in one alignment (using the cursor, or <strong><a
56 href="../calculations/sorting.html">"Calculate→Sort")</a></strong>
57 is also applied to the other
59 <li>Editing (gap insertion / deletion) in the protein alignment
60 is reflected in the cDNA (but not vice versa)</li>
61 <li>Any trees imported or created with <strong><a
62 href="../calculations/tree.html">"Calculate Tree"</a></strong> on
63 one of the views allow both cDNA and Protein views to be grouped,
66 <li>To allow for the different widths in cDNA and Protein
67 alignments, the <strong><a href="../menus/alwformat.html">"Format→Font"</a></strong>
68 menu option has an option 'Scale protein residues to codons'. This
69 option will make each protein residue the same width as a DNA
70 codon (so the alignments 'line up' vertically).<br/><br/>
71 <a name="mirror"/>The 'Use same
72 font for cDNA and peptide' checkbox, when enabled, ensures that font or
73 font-size changes in either the cDNA or Protein alignment will also
74 be mirrored. (<em>Added in 2.10.2</em>)
76 <li><strong>"View→Protein"</strong> (in the cDNA panel)
77 or <strong>"View→Nucleotide"</strong> (in the protein panel)
78 allows you to show or hide one or other of the linked alignment
80 <li>Panel heights are adjusted dragging the divider between
81 them using the mouse</li>
82 <li><a href="../menus/alwview.html"><strong>"View→New
83 View / Expand Views / Gather Views"</strong></a> behave as for a normal
84 alignment window, but always create new views as Split Frames</li>
87 An alignment annotation row on the protein alignment shows the <strong><a
88 href="../calculations/consensus.html">cDNA consensus</a></strong> for
89 each peptide column.<br /> This consensus may reveal variation in
90 nucleotides coding for conserved protein residues.
93 <a name="opensplit" />
95 <strong>Opening a Split Frame View</strong>
97 <p>A Split Frame View can be opened in one of the following ways:</p>
99 <strong><em>Add Sequences</em></strong>
102 If you add (coding) DNA sequences to an open peptide alignment, or
103 vice versa, <em>and</em> at least one DNA sequence translates to one
104 of the peptide sequences, then the option to open in a split window
105 is offered. The DNA may include start and/or stop codons, but no
106 non-coding (intron) sequence.<br> If more than one cDNA variant
107 is present in the alignment, Jalview will first try to match these
108 to protein sequences based on any retrieved cross-references, and
109 failing that, pairwise as they are ordered in the alignments.
110 <p>This option is available in Jalview Desktop (when adding
111 sequences by any supported method), and Jalview applet (adding from
112 textbox). The additional options below apply to Jalview Desktop
116 <strong><em>Translate as cDNA</em></strong>
119 Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Translate
120 as cDNA"</a></strong> is available for a nucleotide alignment. Selecting this
121 option shows the DNA and its calculated protein product in a Split
126 <strong><em>Get Cross-References</em></strong>
129 Menu option <strong><a href="../menus/alwcalculate.html">"Calculate→Get
130 Cross-References"</a></strong> is available for fetched sequences which have
131 cross-references to other databases. On selecting protein
132 cross-references (for a cDNA alignment), or DNA xrefs (for peptide),
133 a Split Frame view is opened showing cDNA and peptide.
137 <strong><em>Realign a Split View</em></strong>
139 <p>If you invoke a web service to realign either half of a Split
140 Frame, then the resulting realignment is displayed in a new Split
143 <li>the alignment you chose to realign (for example, peptide)
144 is displayed as aligned by the external web service</li>
145 <li>Jalview reconstructs the alignment of its complement (in
146 this case, cDNA) by inserting gaps in the corresponding positions</li>
149 <a name="reconalignment" /><strong>Reconstructed
153 Reconstructed alignments are typically <em>not</em> the same as the
154 alignment produced by aligning the complement sequence set directly
155 with the external service. However, in the case of protein
156 alignments, a reconstructed cDNA alignment is often more reliable
157 than one calculated without coding information. Reconstructed cDNA
158 alignments are also more informative than the original protein
159 alignment when calculating phylogenetic trees or performing other
160 kinds of molecular evolution analysis.
163 <em>Split Frame Views were introduced in Jalview 2.9</em>