X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2FsplitView.html;h=be1bd662eaa9c87d5ba46d475532e029773139e7;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=80e27b07b18a680e0d2598805075412b3a3ab52d;hpb=25687914d19af3fc0057e9465a29d2dc6a94f27a;p=jalview.git diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html index 80e27b0..be1bd66 100644 --- a/help/html/features/splitView.html +++ b/help/html/features/splitView.html @@ -23,76 +23,143 @@
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.
-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.
+
+
+ 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 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.
-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 | -
- Split Frame Views were introduced in Jalview 2.9 -
-- Example files for cDNA/Protein: estrogenReceptorProtein.fa - and estrogenReceptorCdna.fa - taken from xxx. -
++ 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 +