Split Frame Views

• 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)
• on "Calculate Tree" in either alignment, grouping, colouring and sorting by tree are applied to both
• the "Format→Font" menu option has an option 'Scale protein residues to codons'; select this option to make each protein residue the same width as a DNA codon (so the alignments 'line up' vertically)
• menu option "View→Protein" (in the cDNA panel) or "View→Nucleotide" (in the protein panel) allows you to show or hide the complementary alignment
• you can adjust panel heights by dragging the divider between them using the mouse
• menu options "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 'aligns' its complement (in this case, cDNA) similarly, by inserting corresponding gaps
  • NB this is not the same as aligning the complement using the external service, which may give different results

Applet

To see a split frame view in the Jalview applet, provide these applet parameters:

Parameter	Value	Description
file	path to an alignment file	a cDNA (or protein) alignment
file	path to an alignment file	a protein (or cDNA) alignment
enableSplitFrame	true	to enable the Split Frame feature

If compatible sequences are present in the input alignments, Jalview will open a Split Frame view.
If not, only the first alignment will be opened (an error message is written to the Java console).

Split Frame Views were introduced in Jalview 2.9