GeneMark.hmm Manual

Return to GeneMark.hmm (Prokaryotic)

Using Prokaryotic GeneMark.hmm gmhmmp

The GeneMark.hmm program is started by 'gmhmmp'. Typing this command without any parameters will print out a list of options .
The general format for executing GeneMark.hmm is:

gmhmmp [ options ] sequence-file

The default options may be specified using shell environment variables. If no options are provided, GeneMark.hmm will use a set of default options. If there is no default gene model defined, you MUST specify the name of the model you wish to use.

If you want to find coding regions in a sequence file named sequence.fna using a gene model named ecoli.mod and default parameters, you would type:

gmhmmp -m ecoli.mod sequence.fna

The sequence file MUST be a Fasta type file format.

Prokaryotic GeneMark.hmm Options :

-m model-file Specifies the model's file to use. The program will look for model-file in current working directory. If the file is not found, search will be continued in the file path indicated in the environment variable MATPATH (if specified.)
-r Specifies the use of an ribosomal binding site (RBS) model. If this option is specified, the RBS model must be present in the specified model file
-o output-file Specifies the filename for output data predicted genes/exons in terms of sequence positions. If this option is not specified, the output file ' sequence-file.lst ' will be created by default.

Environment Variables Recognized by GeneMark.hmm

MATPATH The list of directories in which to search for GeneMark models. This takes the same form as the standard PATH variable.
DEFMAT_HMMP The name of the model file to be used by GeneMark.hmm if none is specified with '-m' options.
i.e. DEFMAT_HMMP = ecoli.mod.

next: The Prokaryotic GeneMark.hmm Output

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