Online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology
I think that you could try a similar approach to GSFS:


use transduction in proteins (if you don't know star code, then you must use 3 strings for each gene)
use a basic tool (a stand alone like UNIPROT tools) to identify the proteic domain type (chain alpha, ..)
divide the genes by proteic domain type (pdt): which contains which pdt and the pdt order frequencies


Now, you could use DAVID or similar (try wconsensus: it's old, basic but very custom) to compare similar sequence and obtain your scores.