Unit

UNIT 4.5 Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm

  1. Mark Borodovsky1,
  2. Ryan Mills2,
  3. John Besemer2,
  4. Alex Lomsadze2

Published Online: 1 MAY 2003

DOI: 10.1002/0471250953.bi0405s01

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Borodovsky, M., Mills, R., Besemer, J. and Lomsadze, A. 2003. Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm. Current Protocols in Bioinformatics. 1:4.5:4.5.1–4.5.16.

Author Information

  1. 1

    School of Biology and School of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia

  2. 2

    School of Biology, Georgia Institute of Technology, Atlanta, Georgia

Publication History

  1. Published Online: 1 MAY 2003
  2. Published Print: MAR 2003

This is not the most recent version of the article. View current version (1 SEP 2011)

Abstract

In this unit, the GeneMark and GeneMark.hmm programs are presented as two different methods for the in silico prediction of genes in prokaryotes. GeneMark can be used for whole genome analysis as well as for the local analysis of a particular gene and its surrounding regions. GeneMark.hmm makes use of Hidden Markov models to find the transition points (boundaries) between protein coding states and noncoding states and can be efficiently used for larger genome sequences. These methods can be used in conjunction with each other for a higher sensitivity of gene detection.