The GeneMark family of gene finding programs has been used for prokaryotic genome annotation since
1995 when GeneMark contributed to launching the genomic era by providing automatic gene annotation of complete genomes of
Haemophilus influenza, Methanoccus jannaschii as well as Escherichia coli and Bacillus subtilis.
In GeneMark.hmm, 1,3 the second generation of GeneMark, the DNA sequence is interpreted as a realization
semi-Markov model with genome specific parameters. Then the maximum likelihood parse of the sequence into protein-coding and
non-coding regions is generated by an optimization algorithm. Note that the genome specific parameters of the model are
determined from the submitted DNA sequence 2,3.