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GeneMark-ES Gene Finding

The GeneMark-ES Gene Finding plugin offers an innovative approach to finding genes in eukaryotic genomes along with solving the parameter estimation problem by iterative self-training.

GeneMark Gene Finding online manual

GENE PROBE Inc., the developers of the core components of GeneMark-ES, have developed an original implementation of the Viterbi algorithm for hidden semi-Markov Model of the eukaryotic genomic sequence. Gene Probe, Inc. has created and refined algorithms for gene prediction in genomic sequences for more than twenty-five years. GeneMark-ES gene finding plugin was further optimized for gene finding in fungal genomes.

GeneMark-ES is an ab initio gene finder designed to predict protein coding genes possibly interrupted with introns, a typical feature of gene organization in  eukaryotic genomes. The algorithm parameters are genome-specific and are determined by unsupervised training on a given (novel) genomic sequence. The GeneMark.hmm algorithm uses a hidden semi-Markov model describing the functional and structural organization of a eukaryotic sequence.

Accurate gene finding in eukaryotes made easy

  • The GeneMark-ES gene finding plugin provides full automation. All parameters necessary for analysis are automatically trained.
  • The GeneMark-ES plugin can be readily connected with the Extract Annotations tool and the BLAST tools of QIAGEN CLC Genomics Workbench or QIAGEN CLC Genomics Server.


Lomsadze A., et al. (2005) Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Research 33, 6494–6506.

Ter-Hovhannisyan V., et al. (2008) Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Research 18, 1979–1990.



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