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@ed.ac.uk

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

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@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of rob van nues <rob.van-nues@ed.ac.uk>
Sent: 07 January 2016 12:44
To: Jalview-discuss@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@ed.ac.uk

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

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

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

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@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@jalview.org
<jalview-discuss-bounces@jalview.org> on behalf of rob van nues
<rob.van-nues@ed.ac.uk> Sent: 07 January 2016 12:44 To:
Jalview-discuss@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@ed.ac.uk

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

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@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@ed.ac.uk

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

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.

pastedImage.png

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@ed.ac.uk
Sent: 08 January 2016 11:07
To: Mungo Carstairs (Staff)
Cc: Jalview-discuss@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@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@jalview.org
jalview-discuss-bounces@jalview.org on behalf of rob van nues
rob.van-nues@ed.ac.uk Sent: 07 January 2016 12:44 To:
Jalview-discuss@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@ed.ac.uk

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


Jalview-discuss mailing list
Jalview-discuss@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@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