Split Frame Views
-Coding DNA (cDNA) and its protein product can be displayed in a split view, with cDNA above and protein below. The two alignments are -linked, with these features supported: -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.
+ 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: +
+ 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.
+ ++ 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.
-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. +
-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. +
-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 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.
-Split Frame Views were introduced in Jalview 2.?.?
++ 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.
++ 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 +