Bacterial Operon and Gene Prediction.
FgenesB - Suite of Bacterial Operon and Gene Finding Programs
FgenesB is the most accurate ab initio prokaryotic gene prediction engine (see Table 1 at the bottom for its comparison with two other popular gene prediction programs). FgenesB gene prediction algorithm is based on Markov chain models of coding regions and translation and termination sites. The program uses genome-specific parameters learned by FGENESB-train script, which requires only DNA sequence from genome of interest as an input. (If you need parameters for your new bacteria, please contact Softberry.) FgenesB also includes simplified prediction of operons based only on distances between predicted genes.
For community sequence annotation, ABsplit (www.softberry.com/berry.phtml?topic=absplit&group=programs&subgroup=gfindb) program can be used that separates archaebacterial and eubacterial sequences.
FgenesB was used in first ever published bacterial community annotation project: see Tyson et al., (2004) Nature 428(6978), 37-43.