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Eukaryotic Gene Prediction Using GeneMark.hmm‐E and GeneMark‐ES

2011; Wiley; Volume: 35; Issue: 1 Linguagem: Inglês

10.1002/0471250953.bi0406s35

1934-340X

Mark Borodovsky, Alex Lomsadze,

Chromosomal and Genetic Variations

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.