Microbial Genome Annotation Tools

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 of the hidden 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.

  • 1 Lukashin AV, Borodovsky M. 1998. GeneMark.hmm: new solutions for gene finding., Nucleic Acids Research 26: 1107-1115.
  • 2 Besemer J, Borodovsky M. 1999. Heuristic approach to deriving models for gene finding., Nucleic Acids Research 27: 3911-3920.
  • 3 Besemer J., Lomsadze A. and Borodovsky M. 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Research, 29: 2607-2618.

  • More about the GeneMark line.

    Upload your sequence from file:

    Or copy/paste your sequence FASTA here:

    Additional parameters:
    Genetic code: Shape:
    11 (Bacteria, Archaea)
     4 (Mycoplasma/Spiroplasma)

    25 May 2015, 14:42