Split Frame Views

Jalview provides a special viewing mode to show Coding DNA (cDNA) and protein product alignments as a split view, with cDNA above and protein below. The two alignments are linked, allowing editing and analysis to be performed at both the peptide and nucleotide level. Linked protein alignments also have an additional cDNA Consensus annotation row, showing the distribution of codons at each column of the protein alignment.

Split Frame views can be created in a number of ways. In the Jalview Desktop, Split Frame views are saved in Jalview Projects, like any other alignment view.

Virtual Sequence Features

Since Jalview 2.11.1, sequence features displayed in either CDS or Protein can be shown as 'Virtual Features' mapped onto the other view. Features describing non-synonymous genomic sequence variation in coding regions are dynamically translated when shown in the protein view.

The display of virtual features and whether they are rendered below or above features local to the aligned sequences is controlled by a check box shown in the view's Sequence Feature Settings dialog box. For convenience, Protein and CDS feature settings for a linked CDS/Protein view are shown as tabs in a single dialog box, allowing easy access to display and filter settings for each view.

CDS and Protein feature settings tabs and corresponding views showing 'Virtual Features' from each view overlaid on the other (created with Jalview 2.11.1.0).

When virtual features are enabled, they are also shown on any linked 3D structure views when 'Colour by Sequence' is enabled, and exported as GFF and Jalview Features files (mapped to their associated virtual coordinates). Both the original and the mapped locations are also included in Sequence Feature Reports.

Operations supported in Split Frame Mode

Split Frame views allow the following:

- Mouseover or scrolling of either alignment is followed by the other (unless you turn off "View→Automatic Scrolling")
- On selecting rows, columns or regions in one alignment, the corresponding selection is made in the other
- Sequence ordering in one alignment (using the cursor, or "Calculate→Sort") is also applied to the other
- Editing (gap insertion / deletion) in the protein alignment is reflected in the cDNA (but not vice versa)
- Any trees imported or created with "Calculate Tree" on one of the views allow both cDNA and Protein views to be grouped, coloured or sorted.
- To allow for the different widths in cDNA and Protein alignments, the "Format→Font" menu option has an option 'Scale protein residues to codons'. This option will make each protein residue the same width as a DNA codon (so the alignments 'line up' vertically).
- The 'Use same font for cDNA and peptide' checkbox, when enabled, ensures that font or font-size changes in either the cDNA or Protein alignment will also be mirrored. (Added in 2.10.2)
- "View→Protein" (in the cDNA panel) or "View→Nucleotide" (in the protein panel) allows you to show or hide one or other of the linked alignment panels.
- Panel heights are adjusted by dragging the divider between them using the mouse
- "View→New View / Expand Views / Gather Views" behave as for a normal alignment window, but always create new views as Split Frames

An alignment annotation row on the protein alignment shows the cDNA consensus for each peptide column.
This consensus may reveal variation in nucleotides coding for conserved protein residues.

Opening a Split Frame View

A Split Frame View can be opened in one of the following ways:

Add Sequences

If you add (coding) DNA sequences to an open peptide alignment, or vice versa, and at least one DNA sequence translates to one of the 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) sequence.
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.

This option is available in Jalview Desktop (when adding sequences by any supported method), and Jalview applet (adding from textbox). The additional options below apply to Jalview Desktop only.

Translate as cDNA

Menu option "Calculate→Translate as cDNA" is available for a nucleotide alignment. Selecting this option shows the DNA and its calculated protein product in a Split Frame view.

Get Cross-References

Menu option "Calculate→Get Cross-References" is available for fetched sequences which have cross-references to other databases. On selecting protein cross-references (for a cDNA alignment), or DNA xrefs (for peptide), a Split Frame view is opened showing cDNA and peptide.

Realign a Split View

If you invoke a web service to realign either half of a Split Frame, then the resulting realignment is displayed in a new Split Frame.

- the alignment you chose to realign (for example, peptide) is displayed as aligned by the external web service
- Jalview reconstructs the alignment of its complement (in this case, cDNA) by inserting gaps in the corresponding positions

Reconstructed Alignments

Reconstructed alignments are typically not the same as the alignment produced by aligning the complement sequence set directly with the external service. However, in the case of protein alignments, a reconstructed cDNA alignment is often more reliable than one calculated without coding information. Reconstructed cDNA alignments are also more informative than the original protein alignment when calculating phylogenetic trees or performing other kinds of molecular evolution analysis.

Split Frame Views were introduced in Jalview 2.9