Jalview 2.5 Release

Jalview Discussion
1

I installed Jalview 2.5 (previously using 2.4) and now the Conservation and the Quality histograms fail to appear automatically. They appeared fine with the same input files when running version 2.4. Any suggestions?

Mark

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Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
University of Michigan

Biophysics, 3040 Chemistry Building
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

saper@umich.edu phone (734) 764-3353 fax (734) 764-3323
http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

2

Hello Mark. Thanks for the email.

I installed Jalview 2.5 (previously using 2.4) and now the Conservation and the Quality histograms fail to appear automatically. They appeared fine with the same input files when running version 2.4. Any suggestions?

Several - but no definite cures. If the annotation was displayed before for precisely the same protein sequence alignment, then something has happened to your preferences after upgrading. You should be able to re-enable conservation and quality in the Visual tab of the preferences dialog box (Tools->Preferences from the desktop window).

If that doesn't help, then could you send me a copy of an alignment where you have this problem ? It would also help if you can send me the .jalview_properties file that you have. A couple of bugs relating to the alignment annotation display have been fixed recently - you can try out the latest version from here:
http://www.compbio.dundee.ac.uk/users/ws-dev1/jalview/release/webstart/jalview.jnlp

Jim.

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On 06/06/2010 22:17, Mark A Saper wrote:

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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.

3

The link that you indicated does not exist. Could you check it?

Ah - a typo - the url should be:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/release/webstart/jalview.jnlp

I uninstalled versions 2.4 and 2.5 (I think), and reinstalled 2.5. Then I played around with the example.jar file and with the preference settings. Anyway, it started to work.
   

hmm. ok. that doesn't sound like a very positive experience - it should be quite clear what's going on. One thing I should make clear is that the quality and Conservation score are protein specific - so if you are working with sequences with greater than 85% [ACTG] content, Jalview will think you're working with nucleic acids, and disable the conservation and quality annotation.

Question--- I want to indicate residue positions that are in a potential binding site for sequence 1. Is there an easier way to do this besides creating one of the feature files? I'm not sure how to map residue number with column number in the file. Any suggestions?
   

You can interactively create features by selecting regions of the sequence(s) with a putative binding site, right clicking on each selection and following the 'selection' submenu to the 'Create features' menu item. If you'd like to work through a tutorial that covers this, then take a look at the Jalview manual:

http://www.jalview.org/tutorial/TheJalviewTutorial_screen.pdf

I'm currently updating the manual for version 2.5, but this is mostly cosmetic - and the exercises should work fine in both versions.

I'm sorry the upgrade hasn't been such a smooth experience. Hopefully, the next upgrade will be less of a problem!
Jim.

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On 07/06/2010 03:20, Mark A Saper wrote:

--
-------------------------------------------------------------------
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.