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.

FgenesB is gene finding part of FgenesB_Annotator which is a package for automatic annotation of bacterial genomes and includes the following features:
• automatic training of gene finding parameters for new bacterial genomes using only genomic DNA as an input (optionally, pre-learned parameters from related organism can be used);
• mapping of tRNA and rRNA genes;
• highly accurate Markov chains-based gene prediction;
• prediction of promoters and terminators;
• operon prediction based on distances between ORFs and frequencies of different genes neighboring each other in known bacterial genomes, as well as on promoter and terminator predictions;
• automatic annotation of predicted genes by homology with protein (COG, NR) databases.

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.