GeneMark.hmm Manual

Return to GeneMark.hmm (Eukaryotic)

Using Eukaryotic 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 HUMBRCA1 using a gene model named human.mtx and default parameters, you would type:

gmhmmp -m human.mtx HUMBRACA1

The sequence file MUST be a Fasta type file format.

Eukaryotic 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.)
-b start-position Sets the beginning position in the sequence for analysis. Default value is 1.
-e end-position Sets the last position in the sequence for analysis. Default value is the last position in the sequence.
-c Requests to calculate G+C percentage based on the range indicated by -e and -b options. By default the G+C percentage is calculated on the whole sequence.
-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.
-n nucleotide-file Specifies the filename for output data containing the nucleotide sequences of the predicted genes.
-l Shows the license expiration date.

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_HMME The name of the model file to be used by GeneMark.hmm if none is specified with '-m' options.
i.e. DEFMAT_HMME = human.mat.

next: The GeneMark.hmm Output

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