I'm trying to annotate a genome to find all genes with a specific function. I have a FASTA and the read FASTQs - I'd like to assign the functional group of the identified proteins (e.g. Kegg orthology) automatically.
For more context, I have whole genome sequences of bacteria - I'm trying to find all genes involved in membrane transport. I'd either like a tool to retrieve gene ontologies from a list of gene names (input: genA output: Membrane Transport), or a tool that outputs the function as part of the annotation pipeline (e.g. genbank output with GO function defined).
Or posed in a different way, how would you identify all genes with a specific function from prokaryotic whole genome sequence data?
Are there any scripts that can do this?