[BioC] Reading GFF files into R and GenomeGraphs

Michael Dondrup Michael.Dondrup at bccs.uib.no
Thu Jul 30 09:52:16 CEST 2009

Dear BioC list,

I'm trying to use the package GenomeGraphs to visualise custom genome  
data (genome not in public databases). In the corresponding  
publication to genomegraphs (Durinck et al. BMC Bioinformatics, 2009 )  
I found the partial clue: "... genomic annotation encoded in GFF files  
can be easily used to create a custom AnnotationTrack object for  
visualization... region start, and end positions need to be given, as  
well as how these regions are to be grouped."
This leaves me with two questions:
- I have no idea how to parse a GFF file, is there a GFF parser in  

- If I have such GFF file for a genome, how can I create such an  
AnnotationTrack with all CDS?

Hope somebody can help me with one of this.


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