Hi Karin, So one thing you can look at for KEGG data is the KEGGSOAP package. And since you just sequenced these organisms, AnnotationDbi might not have been the best tool anyways since it is designed to support gene centric annotations and a sequencing project is inherently genome centric. So you might want to look at the rtracklayer package which should let you have access to track data from this organism. There actually ARE some tracks for this microbe at the "other" UCSC genome browser which you can find here:
http://microbes.ucsc.edu/cgi-bin/hgTracks?hgTracksConfigPage=notSet?org=Lactococcus+lactis&db=lactLact&hgsid=305813 There is nothing for KEGG at UCSC (on this organism) though. To map to KEGG, you are going to have to get the sequences for your organism mapped to the appropriate gene IDs used by KEGG 1st. Hope this helps, Marc Karin Bjerre wrote: > Dear all, this is really basic questions, but I am new in the area. > > I have sequenced two strains of Lactococcus lactis, and now I would like > to annotate them. As I understand, the annotation software ?annotationDbi? > does not support this organism. Some Lactococcus lactis strains have been > sequenced and are available at NCBI, and pathways are present in KEGG. > > Well, I guess it its possible to annotate within R/Bioconductor, do you > have any suggestions how I should do? > > Best regards > > /Karin > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
