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Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.5. doi: 10.1002/0471250953.bi0405s01.

Prokaryotic gene prediction using GeneMark and GeneMark.hmm.

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School of Biology and School of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.


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.

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