Related to my previous post, I have a list of genes that have been pooled out from around 60 different bacterial species based on some criteria. Now, I would like to see if there is any functional enrichment in this group. My idea was to use DAVID, however none of the locus_tag inputs are recognized. When I manually try some of them in the NCBI's Gene database, they are found but often marked as "discontinued" or "updated".
Any idea how to work around this problem? locus_tag is the only common gene flag among all these different bacterial species. Is there another tool for functional clustering that will either accept locus_tag or is there a way around to translate those locus_tag 's into something more readable by DAVID?
Also, I was thinking of extracting the amino acid sequence of the hits and use that as query to get protein domain signatures. Is there a tool that performs functional clustering based on protein signatures and domains?
Thank you, TP