Program for predicting multiple genes in genomic DNA sequences using HMM gene model plus homology with known protein
The program can be used if you know protein sequence similar to protein which is predicted for a gene in your sequence. First, run any ab initio gene finding program such as Fgenes or Fgenesh. Then, run BLASTP DB search with each predicted exon. Any true predicted exon can provide you with known similar proteins, if such proteins exist in the DB. Take sequence of homologous protein and run Fgenesh+. The accuracy of gene prediction can be up to 100% depending of how similar the predicted and DB protein are.