|
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:
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
|