HMM-based gene structure prediction (multiple genes, both chains)
Fgenesh is the fastest (50-100 times faster than GenScan) and most accurate gene finder available (see the figure and the table in help). In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff et al. (2002) Science 296:79).