[BioC] Using package GenomeGraphs with genomes not in ensemble

Michael Dondrup Michael.Dondrup at bccs.uib.no
Tue Jul 28 16:39:46 CEST 2009

I like the visualisations in the GenomeGraphs package and would like  
to use it to plot
RNA-seq data on a bacterial genome. However, that genome is not in the  
Ensemble database and therefore
cannot be queried using biomart. Has anyone tried to use this package  
and create an annotation
from scratch, e.g. given an EMBL file? Or is this feature eventually  
planned for the future?

My best guess would be to provide an alternative implementation of the  
makeGeneRegion function, which takes an embl file
instead of a mart object. Did anyone try this, or could the authors  
give a recommendation where to start?

Thank you very much

Michael Dondrup
Bergen Center for Computational Science
Computational Biology Unit
Unifob AS - Thormøhlensgate 55, N-5008 Bergen, Norway

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