It is offered in the Colour menu for nucleotide or peptide alignments, but there is associated colour action (or help documentation).
What is it?
m
The University of Dundee is a registered Scottish Charity, No: SC015096
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk
typo
" there is NO associated colour action…"
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk
From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk
Sent: 08 December 2016 09:17:14
To: Jalview Development List
Subject: [Jalview-dev] RNA iteraction type colour scheme
It is offered in the Colour menu for nucleotide or peptide alignments, but there is associated colour action (or help documentation).
What is it?
m
The University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk
Hello Mungo.
typo
" there is NO associated colour action..."
What is it?
Something that was included as prototype in 2.8.2:
http://issues.jalview.org/browse/JAL-1520
But has become broken since then. For the moment it may need to be
disabled in any released version. For instance, see issue raised by Charles:
http://issues.jalview.org/browse/JAL-1895
This should have been fixed back in 2015 for the 2.9 release, at the
same time as you and I were trying to resolve the pseudoknot issue and
linked VARNA display, but we backed off then because of other
priorities. As you can see, nothing else was done.
RNA interaction types are imported via RNAML filed derived from RNA 3D
structures. Anne Menard implemented a prototype as part of her 'Jalview
Summer of Code' in 2012, which encoded the sugar edge interactions as
different RNA base pair symbols. Jalview renders these symbols as
distinct colours already, making the 'RNA interaction colourscheme'
redundant, but the implementation needs to be looked at again because it
doesn't really fit the needs of an RNA alignment analyst. There's also a
conflation in the data encoding, since alignment annotation glyph
symbols are used for both sugar edge and pseudoknot pairings, when in
fact these are not directly coupled. RNA interaction types should also
passed to VARNA in order to display Leontis Westoff notation on each
base pair.
Does that help ?
Jim.
On 08/12/2016 09:18, Mungo Carstairs (Staff) wrote:
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk