论文信息 - 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 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.

Mark Borodovsky | M. Borodovsky | A. Lomsadze | Alex Lomsadze

[1] M. Borodovsky,et al. GeneMark.hmm: new solutions for gene finding. , 1998, Nucleic acids research.

[2] Lawrence R. Rabiner,et al. A tutorial on hidden Markov models and selected applications in speech recognition , 1989, Proc. IEEE.

[3] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.

[4] M. Borodovsky,et al. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. , 2008, Genome research.

[5] M. Borodovsky,et al. Gene identification in novel eukaryotic genomes by self-training algorithm , 2005, Nucleic acids research.

[6] Mark Borodovsky,et al. GENMARK: Parallel Gene Recognition for Both DNA Strands , 1993, Comput. Chem..