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Thomas Lin Pedersen
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70
@thomas-lin-pedersen-5941
Last seen 9.0 years ago
Copenhagen, Denmark
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