GeneMark.hmm for eukaryotic genomes (with introns) version 3
Copyright (c) 2001, GeorgiaTech
Copyright (c) 2001, Gene Probe, Inc.
All Rights Reserved
Algorithm GeneMark.hmm predicts protein coding genes within a eukaryotic DNA sequence.
Lomsadze A., Ter-Hovhannisyan V., Chernoff Y. and Borodovsky M.
"Gene identification in novel eukaryotic genomes by self-training algorithm."
Nucleic Acids Research, 2005 Nov; 33(20):6494-506
Ter-Hovhannisyan V., Lomsadze A., Chernoff Y. and Borodovsky M.
"Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training."
Genome Research, 2008 Dec; 18(12):1979-90
GeneMark.hmm eukaryotic 3 is distributed under Creative Commons Attribution NonCommercial ShareAlike 4.0 License. See the full text of the license.
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./gmhmme3
GeneMark.hmm eukaryotic, version 3.68.pub
Usage: gmhmme3 [options] <sequence file>
required parameters:
-m <model file>
optional parameters:
-o <output file>
-p write protein translation
-n write nucleotide sequence
-b <output file> output statistics of predicted introns
-d <file name> input for GeneMark.hmm plus
-s <string> sequence tag in GFF output format
-f <format> output prediction in [lst|gff3|gtf] format; default [lst]
-k <number> value for soft-mask penalty
developer options:
-z trace back seqid and position
-w <number> minimum gene length
-r report best path probability
-v verbose
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