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.

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)
• "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 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.

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