Split Frame Views

From c430b05635b0c539d44db6383cc7e742c741adfb Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 20 Apr 2015 15:41:27 +0100 Subject: [PATCH] JAL-1701 first draft of help page for Split View (not linked in) --- help/html/features/splitView.html | 74 +++++++++++++++++++++++++++++++++++++ help/html/menus/alwcalculate.html | 10 ++++- 2 files changed, 83 insertions(+), 1 deletion(-) create mode 100644 help/html/features/splitView.html diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html new file mode 100644 index 0000000..c9ce093 --- /dev/null +++ b/help/html/features/splitView.html @@ -0,0 +1,74 @@ + + + +Split Frame Views + + +

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: +

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)

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.

+ +

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 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
+

+ + +

Split Frame Views were introduced in Jalview 2.?.?

+ + diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 7b95a24..50bb37b 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -82,7 +82,15 @@ When selected, these numbers are parsed into sequence associated annotation which can then be used to sort the alignment via the Sort by→Score menu.
- +

Translate as cDNA (not applet)
This option is visible for nucleotide alignments. + Selecting this option shows the DNA's calculated protein product in a new window. Note that the + translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the + standard genetic code (any incomplete final codon is discarded). + You can perform this action on the whole alignment, + or selected rows, columns, or regions.

Get Cross-References (not applet)
This option is visible where sequences have cross-references to + other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries. + Select the database to view all cross-referenced sequences in a new window.

Autocalculate Consensus
For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy -- 1.7.10.2