Adding colour bars above an alignment to indicate different subdomains

Hi,

I’m a new Jalview user and would like to add colour bars above an alignment to indicate different subdomains (effectively as a background to the scale).

Here is an example of what I want to do;

http://www.biomedcentral.com/content/supplementary/1471-2148-10-27-s5.png

That’s supplementary figure 1 from this paper; http://www.biomedcentral.com/1471-2148/10/27 if that link doesn’t work.

Any help would be appreciated,

Thanks,
Aoife

PS I noticed another post which mentioned a problem with inserting gaps by dragging with the mouse. I also couldn’t do this.

Aoife McMahon

PhD student
Kind Lab
School of Biomedical Science
Hugh Robson Building
George Sq
Edinburgh
EH8 9XD

0131 6503110

Hello Aoife - sorry I didn’t reply to this earlier.

I’m a new Jalview user and would like to add colour bars above an alignment to indicate different subdomains (effectively as a background to the scale).

Here is an example of what I want to do;

http://www.biomedcentral.com/content/supplementary/1471-2148-10-27-s5.png

That’s supplementary figure 1 from this paper; http://www.biomedcentral.com/1471-2148/10/27 if that link doesn’t work.

Unfortunately, this isn’t possible. The only thing jalview can render above the alignment is the alignment ruler and the column selection, currently. However, there is a chance it will be added to Jalview in the not-too distant future - probably as an extension to the existing group annotation model.

PS I noticed another post which mentioned a problem with inserting gaps by dragging with the mouse. I also couldn’t do this.

This is almost certainly because you are editing inside a selected area, in which case the ‘locked editing’ constraint applies: http://www.jalview.org/help/html/editing/index.html

I hope this helps!
Jim.

···
-- 
-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.

Okay, I guess the figure I attached was made by adding to the alignment in photoshop or something.

Thanks again

Quoting Jim Procter <jprocter@compbio.dundee.ac.uk>:

···

Hello Aoife - sorry I didn't reply to this earlier.

On 25/05/2010 20:08, Aoife McMahon wrote:

I'm a new Jalview user and would like to add colour bars above an alignment to indicate different subdomains (effectively as a background to the scale).

Here is an example of what I want to do;

_http://www.biomedcentral.com/content/supplementary/1471-2148-10-27-s5.png_

That's supplementary figure 1 from this paper; http://www.biomedcentral.com/1471-2148/10/27 if that link doesn't work.

Unfortunately, this isn't possible. The only thing jalview can render
above the alignment is the alignment ruler and the column selection,
currently. However, there is a chance it will be added to Jalview in
the not-too distant future - probably as an extension to the existing
group annotation model.

PS I noticed another post which mentioned a problem with inserting gaps by dragging with the mouse. I also couldn't do this.

This is almost certainly because you are editing inside a selected
area, in which case the 'locked editing' constraint applies:
http://www.jalview.org/help/html/editing/index.html

I hope this helps!
Jim.

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

--
Aoife McMahon

PhD student
Kind Lab
School of Biomedical Science
Hugh Robson Building
George Sq
Edinburgh
EH8 9XD

0131 6503110

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

yes. That was the main reason for having EPS export in jalview :slight_smile: However, its truly a pain to do this for several regions in the alignment. Its also kind of crazy since the domain information is already buried in some sequence annotation - unfortunately there are quite a few other things I have to do before I can get around to extending the alignment layout to do this.

Jim.

···

On 02/06/2010 14:47, Aoife McMahon wrote:

Okay, I guess the figure I attached was made by adding to the alignment in photoshop or something.

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

The message and the dialog box indicate that there was a problem contacting the server that provides the web service. This is because we actually took the servers down for a 24 hour maintenance period on Friday evening at 18:00. Everything should be working again now, so feel free to try again.

Your confusion does highlight the lack of a Jalview web service health-check function. Its possible to use a web browser to check if the services are up, running and (in some cases) whether they are accepting jobs, but Jalview doesn't tell you how to do it. I'll probably document any developments in this direction on this feature request: http://issues.jalview.org/browse/JAL-201

Jim.

···

On 04/12/2010 20:47, Christian Feller wrote:

Hello Jim,

some time ago I used extensively Jalview for alignments and secondary
predictions. Now I wanted to use it again but I always get the same error
message: Server Error (try later).

I am doing the follow: File-->InputAlignment--> From Textbox

There I put in some sequences in FASTA format

E.g.

test1

Eedql

test2

Ehhedql

The detailed output is:

Alignment of Cut& Paste input - FASTA
Job details
Failed to submit sequences for alignment.
It is most likely that there is a problem with the server.
Just close the window

Is there any local problem with my computer (I don't think it is my Firewall
since when I switch it off it doesn't work either) or with the Server? Any
way to test this?

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

Hi,

We have posted a shutdown notification a week before the shutdown on JABAWS ([www.compbio.dundee.ac.uk/jabaws](http://www.compbio.dundee.ac.uk/jabaws)) web server front page. As a matter of fact there will be another weekend shutdown in the new year. This information is also published on JABAWS front page. The problem might be that not everyone knows where to look for web services status and planned maintenance info. There is no obvious link from Jalview pages to JABAWS web site. 
	On the other hand, the link to JABAWS will only work for as long as web site is up, which was not the case during the latest maintenance as the whole computing infrastructure was on maintenance, including JABAWS web site. If you try to connect to any of the compbio web servers including JABAWS during the maintenance you will be presented a notice of the maintenance which gives the time when the service is restored. However, it is not specific to JABAWS. I think the independent account elsewhere like a twitter feed may be a better way of communicating infrastructure maintenances. 

Regards, 
Peter

Hi All;

I am new to jalview. I want to edit gapes according to my desire.Some
hints would be highly appreciated.

Regards;

Bashir

···

On Mon, December 6, 2010 13:39, Peter Troshin wrote:

Hi,

We have posted a shutdown notification a week before the shutdown on
JABAWS (www.compbio.dundee.ac.uk/jabaws) web server front page. As a
matter of fact there will be another weekend shutdown in the new year.
This information is also published on JABAWS front page. The problem might
be that not everyone knows where to look for web services status and
planned maintenance info. There is no obvious link from Jalview pages to
JABAWS web site.
  On the other hand, the link to JABAWS will only work for as long as web
site is up, which was not the case during the latest maintenance as the
whole computing infrastructure was on maintenance, including JABAWS web
site. If you try to connect to any of the compbio web servers including
JABAWS during the maintenance you will be presented a notice of the
maintenance which gives the time when the service is restored. However,
it is not specific to JABAWS. I think the independent account elsewhere
like a twitter feed may be a better way of communicating infrastructure
maintenances.

Regards,
Peter

On 05/12/2010 12:41, Jim Procter wrote:

On 04/12/2010 20:47, Christian Feller wrote:

Hello Jim,

some time ago I used extensively Jalview for alignments and secondary
predictions. Now I wanted to use it again but I always get the same
error
message: Server Error (try later).

I am doing the follow: File-->InputAlignment--> From Textbox

There I put in some sequences in FASTA format

E.g.

test1

Eedql

test2

Ehhedql

The detailed output is:

Alignment of Cut& Paste input - FASTA
Job details
Failed to submit sequences for alignment.
It is most likely that there is a problem with the server.
Just close the window

Is there any local problem with my computer (I don't think it is my
Firewall
since when I switch it off it doesn't work either) or with the Server?
Any
way to test this?

The message and the dialog box indicate that there was a problem
contacting the server that provides the web service. This is because we
actually took the servers down for a 24 hour maintenance period on
Friday evening at 18:00. Everything should be working again now, so
feel free to try again.

Your confusion does highlight the lack of a Jalview web service
health-check function. Its possible to use a web browser to check if the
services are up, running and (in some cases) whether they are accepting
jobs, but Jalview doesn't tell you how to do it. I'll probably document
any developments in this direction on this feature request:
http://issues.jalview.org/browse/JAL-201

Jim.

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Jalview-discuss mailing list
Jalview-discuss@jalview.org
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--
Muhammad Bashir Khan
**************************************************
Department for Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria

Austria

Phone: +43(1)427752224
Fax: +43(1)42779522

Hi Bashir

···

On 06/12/2010 22:28, Muhammed bashir Khan wrote:

I am new to jalview. I want to edit gapes according to my desire.Some
hints would be highly appreciated.

There's quite a bit of documentation here:
http://www.jalview.org/documentList.html

You should also check out the 'how do I edit sequences in Jalview' quick reference: http://www.jalview.org/examples/editing.html

Hope that helps!
Jim.

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.