Putative genes can be identified by clustering large groups of sequences by patterns and arranging by mutual similarity or can be inferred by potential TATA boxes.
Putative genes can also be identified by recognizing differences between well-known gene clusters and gene clusters with a unique profiling.
Software tools have been developed in order to automatically identify putative genes. This is done by searching for gene families and testing the validity of uncharacterized genes by comparison to already identified genes.
Protein products can be identified and used to characterize the putative gene that codes for it.