GeneMark Manual

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Using GeneMark gm

The GeneMark program is named 'gm'. Typing the program name without any parameters (or with incorrect parameters) will print out a list of options for use with GeneMark. The list is quite long but only a few will need to be specified on a regular basis when using the program.
The general format for executing GeneMark is:

gm [ options ] sequence-file

If no options are provided, GeneMark will use a set of default options (the default options may be specified using shell environment variables ). There is no default gene model defined for gm, so if it is not specified by the environment, you MUST specify the name of the model you wish to use. Therefore, to find coding regions in a sequence file named cyaY using a gene model named ecoli_4.mat and default parameters, you would type:

gm -m ecoli_4.mat cyaY

The file cyaY may be in any of the following sequence formats: raw sequence, GCG, Genbank, FastA, or EMBL.

In this example, GeneMark would produce two output files: and cyaY.lst which contains a PostScript graphic and list of features respectively, but more about those later...

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