[BioC] extending GenomicFeatures to makeTranscriptDbFrom other sources (i.e. GFF3)

[Cook, Malcolm]

Hi,

GenomicFeatures can create TranscriptDb from ucsc or from BioMart, which I have used to good effect.  Thanks!

My aim is now to perform an analysis with a specific old version of the flybase supplied fly gene annotations (namely, ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.22_FB2009_09/gff/)

Thus, I would like to have a TranscriptDb populated from this GFF3 (it is also available in Chado, if that helps).

Does anyone have already written and willing to share an adaptor for GFF3 (makeTranscriptDbFromGFF3 ??) , or Chado, or suggest another route for me (write my own?).


Thanks,

Malcolm Cook - Stowers Institue for Medical Research


  * http://fb2009_09.flybase.org/
  * ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.22_FB2009_09/gff/
  * http://fb2009_09.flybase.org/static_pages/downloads/archivedata3.html