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. 2011 Sep:Chapter 4:4.6.1-4.6.10.
doi: 10.1002/0471250953.bi0406s35.

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

Mark Borodovsky  1 , Alex Lomsadze  1
Affiliations

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

Mark Borodovsky et al. Curr Protoc Bioinformatics. 2011 Sep.

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).

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Figures

Figure 1
Figure 1
The user interface for the eukaryotic GeneMark.hmm program. Required input includes a DNA sequence in FASTA format, either copied and pasted into the Sequence text box, or uploaded from one’s local drive using the Browse button next to the Sequence File Upload box.
Figure 2
Figure 2
The text output for the Eukaryotic GeneMark.hmm program.
Figure 3
Figure 3
The graphical output from the Eukaryotic GeneMark.hmm program for a region of the example sequence. The six different panels represent the six possible reading frames, three each on the direct and reverse strands.
See this image and copyright information in PMC

References

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