[Bioc-sig-seq] Annotation of the lactococcus lactis genome

Marc Carlson mcarlson at fhcrc.org
Sat Sep 19 01:52:33 CEST 2009

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:


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,


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
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