[Jalview-discuss] Further integration with Varna possible?

Mungo Carstairs (Staff) g.m.carstairs at dundee.ac.uk
Fri Jan 8 11:30:21 GMT 2016


Hi Rob,

Yes, mouseover of the Varna bases highlights them in the Jalview sequence, and vice versa.
Also you can select a range in Jalview and see it highlighted in Varna.

The Varna window title includes the sequence name, if that helps.

If you view the sequence structure (not the alignment trimmed to sequence) then the image caption includes the sequence name as well.

[cid:0d92d0b1-11a6-4946-bc4b-099d2627f4cc]

Mungo

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: rob van nues <rob.van-nues at ed.ac.uk>
Sent: 08 January 2016 11:07
To: Mungo Carstairs (Staff)
Cc: Jalview-discuss at jalview.org
Subject: Re: [Jalview-discuss] Further integration with Varna possible?

Hi Mungo,

Thanks for your response. I knew, I had missed something; just
followed those steps you mentioned and managed to see the VARNA
structure for a sequence as based on the alignment; having the trimmed
version available is grand. Thanks.

I just noticed that you can click on a nt in the Varna structure and
see this highlighted on the sequence in the Jalview panel. Fab. UI-wise,
and with respect to further processing of Varna structure(s), would
it be possible to transfer the sequence identifier to the Title of the
displayed Varna structure? This would make it very obvious what
sequence one is looking at.

My other remarks were about transferring other info (esp.
degree of conservation of a nucleotide) to the Varna structure by means
of say the color map.

Cheers,

Rob



On Fri, 8 Jan 2016 09:24:31 +0000
"Mungo Carstairs (Staff)" <g.m.carstairs at dundee.ac.uk> wrote:

> Hello Rob,
>
> Thanks for this, and just to let you know we're not ignoring you,
> just a bit busy with other issues and short-handed with sick leave
> right now.
>
> Your first problem (can't view generated SS in VARNA) puzzles me, as
> I just tried this and it worked fine.
> - view RNA alignment
> - Web Service | SSP | RNAAlifold
> - consensus SS annotation is added
> - SS annotation per sequence can be displayed with "Annotations |
> Show Sequence Related"
> - VARNA view of sequence SS can be shown by right-clicking on the
> sequence id (whether the annotation is visible or not)
>
> I'll digest your other comments properly and get back to you as soon
> as possible.
>
> Best regards,
>
> Mungo
>
> 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-discuss-bounces at jalview.org
> <jalview-discuss-bounces at jalview.org> on behalf of rob van nues
> <rob.van-nues at ed.ac.uk> Sent: 07 January 2016 12:44 To:
> Jalview-discuss at jalview.org Subject: [Jalview-discuss] Further
> integration with Varna possible?
>
> Hi,
>
> Making alignments of RNAs reveals conservation and thereby possible
> important regions (think of guide-RNA sections of snoRNAs or
> protein-binding regions such as the box C/D regions). This can be
> visualized with the WEB-logo / consensus below the sequence by:
>
> a) tick "autocalculate consensus" under "Calculate"
> b) tick "show annotations" under "Annotations"
> c) tick "show consensus logo" in "autocalculated annotation" under
> "Annotation"
>
> Then, by linking up with RNAalifold, that is
> d) tick "RNAalifold Prediction" in "Secondary Structure prediction"
> under "Web Service",
> you also get common secondary structure elements shown below the
> alignment. By right-clicking on the labels in the margin each
> annotation by itself can be viewed/saved.
>
> All can be saved in the .jvp jalview project-file format, incl. format
> - and colour settings.
>
> This is great.
>
> But I experience some serious limitations that prevent me to make
> more use of all this info. Maybe I missed some ways to do this so any
> info to achieve this will be great.
>
> For example,  I cannot view the generated 2D-structurethis directly in
> VARNA via Jalview (only sequences loaded with structure information
> seems to trigger this option, not sequences with structure information
> added inside the program).
>
> The generated WebLogo can be saved  as part of the complete
> alignment but not as an image by itself (which I would find the most
> useful aspect of having this logo as it abbreviates a space-consuming
> alignment and would bypass the need to do make such a figure on the
> WebLogo site).
>
> Also, the MFE-structure generated by alifold is sometimes not complete
> but manual editing is not possible nor can the dot-bracket line be
> copied for pasting into VARNA manually.
>
> This limitation I bypass by generating a fake-sequence using
> import-from text-box in which I use dot-bracket notation to indicate
> secondary structure elements;
> >structure
> .......((((....))))...........
>
> That line, together with a reference sequence I copy manually
> into VARNA and use it to draw a 2D-structure model. But each
> edit/change will require repeating this copy/pasting manually. VARNA
> itself makes this editing also quite tedious (each edit generates a
> new structure that has to be reformatted).
>
> The biggest lost though, is the conservation-information that is
> embedded in the consensus and web-logo. VARNA allows colouration of
> nucleotides by using a Color Map. But I cannot find an easy way of
> converting the Consensus-WebLogo csv file to a version that could be
> used as a colormap in Varna.
>
> A way around this would possibly be to:
>
> a) create a 'structure field/line' that is read by
> JalView as such (i.e. that triggers the connection with VARNA) in
> which an alifold output can be loaded but that is also editable.
> Ideally this field would allow saving to various RNA-2D formats
> (bracket, stockholm,ct)
> b) create a way to export the weblogo-conservation info to a color-map
> for VARNA (or load this into the VARNA displayed structure).
>
> Does this sound feasible or are other tools at hand I have missed to
> accomplish this???
>
> Cheers,
>
> Rob
>
>
> --
> Dr. R.W. van Nues
>
> SYNTHETIC and SYSTEMS BIOLOGY at EDINBURGH (SynthSys)
>
> The University of Edinburgh
> CH Waddington Building
> Max Born Crescent
> Edinburgh EH9 3BF
>
> Telephone +44 (0)131 651 9018
> E-mail:rob.van-nues at ed.ac.uk
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss at jalview.org
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
>
> The University of Dundee is a registered Scottish Charity, No:
> SC015096
>



--
Dr. R.W. van Nues

SYNTHETIC and SYSTEMS BIOLOGY at EDINBURGH (SynthSys)

The University of Edinburgh
CH Waddington Building
Max Born Crescent
Edinburgh EH9 3BF

Telephone +44 (0)131 651 9018
E-mail:rob.van-nues at ed.ac.uk

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


The University of Dundee is a registered Scottish Charity, No: SC015096
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