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

[Marc Carlson]

Hi Karin,

Sorry about the long delay to reply, but its probably better late than
not at all.  I have actually been busy inventing and testing a solution
just for people like you.  In the devel branch, (soon to be release)
there is a way to solve this problem that has been introduced to
Category and GOstats so that if you have an annotation source you can
still do hypergeometric testing.  You will still need some source of
annotation, it just doesn't have to be an annotation package anymore. 
For your specific critter, I would probably use blast2GO to get GO data
for example.  You can find such data here:

http://bioinfo.cipf.es/b2gfar/

Just search for Lactocuccus.

Now once you have that, you will want to do something like this:

library("GOstats")
library("GSEABase")
library("AnnotationDbi")

frame=GOFrame(yourFrameData,organism="Homo sapiens")
allFrame=GOAllFrame(frame)
gsc <- GeneSetCollection(allFrame, setType = GOCollection())
params <- GSEAGOHyperGParams(name="My Custom GSEA based annot Params",
geneSetCollection=gsc, geneIds = genes, universeGeneIds = universe,
ontology = "MF", pvalueCutoff = 0.05, conditio
nal = FALSE, testDirection = "over")
Over <- hyperGTest(params)


This example assumes that you have a data.frame to start with that
contains GO terms matched with Gene IDs.  It also assumes that your Gene
IDs are unique identifiers so you might want to check that to make
sure.  Some details about what your data.frame should look like are in
the manual page for GOFrame.  I can answer other questions if you have them.


  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
>
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