Open AccessEukaryotic Gene Prediction Using GeneMark.hmm‐E and GeneMark‐ES
Author(s) -
Borodovsky Mark,
Lomsadze Alex
Publication year - 2011
Publication title -
current protocols in bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.535
H-Index - 57
eISSN - 1934-340X
pISSN - 1934-3396
DOI - 10.1002/0471250953.bi0406s35
Subject(s) - annotation , hidden markov model , gene , genome , computational biology , gene prediction , genomic dna , dna sequencing , computer science , coding region , biology , genetics , artificial intelligence
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.