UNIT 4.6 Eukaryotic Gene Prediction Using GeneMark.hmm-E and GeneMark-ES

  1. Mark Borodovsky,
  2. Alex Lomsadze

Published Online: 1 SEP 2011

DOI: 10.1002/0471250953.bi0406s35

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Borodovsky, M. and Lomsadze, A. 2011. Eukaryotic Gene Prediction Using GeneMark.hmm-E and GeneMark-ES. Current Protocols in Bioinformatics. 35:4.6:4.6.1–4.6.10.

Author Information

  1. Georgia Institute of Technology, Atlanta, Georgia

Publication History

  1. Published Online: 1 SEP 2011
  2. Published Print: SEP 2011


This unit describes how to use the gene-finding programs GeneMark.hmm-E and GeneMark-ES for finding protein-coding genes in the genomic DNA of eukaryotic organisms. These bioinformatics tools have been demonstrated to have state-of-the-art accuracy for many fungal, plant, and animal genomes, and have frequently been used for gene annotation in novel genomic sequences. An additional advantage of GeneMark-ES is that the problem of algorithm parameterization is solved automatically, with parameters estimated by iterative self-training (unsupervised training). Curr. Protoc. Bioinform. 35:4.6.1-4.6.10. © 2011 by John Wiley & Sons, Inc.


  • gene finding;
  • hidden Markov model;
  • unsupervised parameter estimation