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Using Eukaryotic GeneMark.hmm
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gmhmmp
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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:
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 :
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-m model-file
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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.)
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-b start-position
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Sets the beginning position in the sequence for analysis. Default value is 1.
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-e end-position
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Sets the last position in the sequence for analysis. Default value is the last position
in the sequence.
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-c
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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.
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-o output-file
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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.
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-n nucleotide-file
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Specifies the filename for output data containing the nucleotide sequences of the
predicted genes.
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-l
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Shows the license expiration date.
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Environment Variables Recognized by GeneMark.hmm
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MATPATH
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The list of directories in which to search for GeneMark models. This takes the same
form as the standard PATH variable.
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DEFMAT_HMME
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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.
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next: The GeneMark.hmm Output
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