Three questions about Jalview

Jalview Discussion
1

Hello Muhammad,

Sorry for the delay in replying, for some reason not all posts to the list make it through to my inbox (some issue with different mail clients?).

  1. The difference between Jalview and JalviewLite is described at http://www.jalview.org/About.

  2. Jalview has no ‘magic button’ to identify protein domains but is intended to support workflows aimed at doing this (amongst others).

For instance in Jalview you can:

  • ​inspect protein sequences that you have collected through BLAST searches or other means

  • call services to align your ‘protein of interest’ with other suspected homologs

  • call services to predict secondary structure

  • display feature annotations (whether retrieved from databases or added by your curation)

  • use a variety of built-in or user-defined colour schemes to highlight different aspects of an alignment

  • calculate and show consensus scores, pairwise identity, trees or Principal Component Analysis

  • show 3D structure (where known and retrieved from PDB or other source) using the JMol or Chimera viewer

http://www.jalview.org/about/documentation has a link to the User Manual with comprehensive exercises which you might find it useful to work through.

  1. Please enable Java Console (Tools | Show Java Console) and capture any error message when trying to save files and we can take a look at this. There could be range of causes such as lacking write permission to the target directory.

Best regards,

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

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

2

Just to follow up on Mungo’s reply to your email Muhammad:

  1. Jalview has no ‘magic button’ to identify protein domains but is intended to support workflows aimed at doing this (amongst others).

I suggest you try ‘Domaination’ - which allows denovo identification of domains by iterative blast: http://www.ibi.vu.nl/programs/domainationwww/

This server allows you to export results to Jalview for further analysis. You could also run interproscan - which we will be including support for in the near future.
http://www.ebi.ac.uk/interpro/search/sequence-search

  1. Please enable Java Console (Tools | Show Java Console) and capture any error message when trying to save files and we can take a look at this. There could be range of causes such as lacking write permission to the target directory.

Please also try webstart launching Jalview via
http://www.jalview.org/builds/latest/webstart/jalview.jnlp

It may be that there is a specific problem with the installAnywhere Jalview installer.
Jim.

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On 30/03/2015 09:09, Mungo Carstairs (Staff) wrote:

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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) 
The University of Dundee is registered Scottish charity: No.SC015096