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:
If no options are provided, GeneMark will use a set of default options (the default
options may be specified using shell
). 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
using a gene model named
and default parameters, you would type:
gm -m ecoli_4.mat cyaY
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:
cyaY.lst which contains a PostScript graphic
and list of features respectively, but more about those later...
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