I have RNAseq data on B. subtilis, and mapped it to the genome so I have gene names and even BSU numbers for all of the genes. So far so good. Now I am struggling to find and assign functional annotations to each, preferably GO annotation.
Despite B. subtilis being a model organism, it is not included in the GO consortium database; they only have E. coli.
KEGG and bsubcyc both have B. subtilis functional annotations, but I cannot find a way to download any flat file from either site that associates each gene with its functional assignments.
How do people do this? What set of bioinformatics skill am I totally unaware of but that seem to be taken for granted? Do people "webpage scrape" for this info from KEGG? Is there a database format I need to learn?