FGENESH++ is our newest gene prediction program that works in following steps: (1) performs ab initio gene prediction using FGENESH algorithm; (2) runs predicted amino acid sequences of all potential exons through NR protein sequence database using DBSCAN-P engine; and (3) runs second round of gene prediction with higher scores assigned to exons homologous to known proteins.
The result is fully automated genome annotation of quality similar to manual annotation. The program is extremely fast - whole human genome is annotated in 20-30 hours on a machine like 500 MHz DEC Alpha. Due to computer resources constraints, we cannot make FGENESH++ available through the web site - you have to use FGENESH+ instead.