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

Abstract

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.