[BioC] Working with non-type strain annotation

[Thomas Dybdal Pedersen]

Hi

I'm doing proteomics on industrial bacterial strains. The genomes of these strains are almost completed (no joining of contigs) and my main genomic data is thus a list of CDS's. I have functionally annotated these using Blast2Go, and have thus GO terms, possibly EC number and Uniprot ID for the closest match for most of the CDS's.

My question is thus: How do I best proceed with this data in the Bioconductor framework, when I want to do things suchs as gene set enrichment analysis etc. Is the best approach to build my own Annotation packages for each strain or is there a simpler 'ad hoc' data structure that supports the same functionality?

It seems that most of the tutorials etc. supposes that you work on type strains (which is also probably true for the most part) where an annotation package is readily available…

best

Thomas