Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES

Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES

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 hav...

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Bibliographic Details
Published in:Current protocols in bioinformatics Vol. Chapter 4; p. 4.6.1
Main Authors: Borodovsky, Mark, Lomsadze, Alex
Format: Journal Article
Language:English
Published: United States 01-09-2011
Subjects:
Algorithms
Computational Biology - methods
Eukaryota - genetics
Genes - genetics
Genome - genetics
Internet
Models, Genetic
Software
Online Access:Get more information
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Summary: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).
ISSN:1934-340X
DOI:10.1002/0471250953.bi0406s35