Hi,
In the past I have used DAVID pathway clustering tool to get enriched clusters of genes for various biological pathways using lists of genes as inputs. Recently, there is a concern that DAVID's annotation may not be up-to-date. I wonder if there is any similar tool that allows genes lists as inputs and uses specific annotation databases(e.g., kegg) for bacteria such as Salmonella and Streptococcus sp.
Thanks
I sympathize with this question even if I work with mainstream genomes. What I like of DAVID is that there is a nice interface for R (RDAVIDWebService) which generates very useful summary tables. Other packages like topGO or GOseq give an output that is much less useful.