title: Prokaryotic gene prediction using GeneMark and GeneMark.hmm.
abstract: In this unit, the GeneMark and GeneMark.hmm programs are presented as two different methods for the in silico prediction of genes in prokaryotes. GeneMark can be used for whole genome analysis as well as for the local analysis of a particular gene and its surrounding regions. GeneMark.hmm makes use of Hidden Markov models to find the transition points (boundaries) between protein coding states and noncoding states and can be efficiently used for larger genome sequences. These methods can be used in conjunction with each other for a higher sensitivity of gene detection.
authors.affiliation: School of Biology and School of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Borodovsky
authors.forename: Ryan
authors.initials: R
authors.lastname: Mills
authors.forename: John
authors.initials: J
authors.lastname: Besemer
authors.forename: Alex
authors.initials: A
authors.lastname: Lomsadze
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D020745:Genome, Archaeal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D008390:Markov Chains; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software