Network generation from fully annotated JGI genome Projects

[a.w...@uni-bayreuth.de]

I would like to generate a network from fully annotated non-model organisms availabe at the Mycocosm portal at JGI-DOE. These genomes regularily provide the following annotations:

Functional Annotations

EC annotations and KEGG pathway annotations

GO annotations

KOG annotations

InterPro domains

Signalp annotations

Is it possible to generate a new network by 'extracting' information from the above annotations? Since we work with fungi, are there some fungal networks available that could serve as a backbone to geneate the new network?

Thanks for suggestions!

[piet molenaar]

Hi,

The CyKEGGParser (http://apps.cytoscape.org/apps/cykeggparser) see image allows you to download networks available also for fungi from the webserver. 

KEGGscape does the same but you should download the pathway file from the KEGG db first (http://apps.cytoscape.org/apps/keggscape)  

Hope this helps,

Piet

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

--

Piet Molenaar
piet...@gmail.com
Department of Oncogenomics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626