Documentation read from 04/17/2019 22:07:27 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_project_model.



Project atomic regulons from model to new genome.



    svr_project_model -a AtomicRegulons -e Effectors -g TargetGenome -m ModelDir

would produce a directory called "MOdelDir" that contained

    atomic.regulons  [ a file defining the projeted atomic.regulons ]
    effectors        [ a file of predicted effectors ]
    errors           [ a log of problems encountered in the projection ]

Command-Line Options

-a AtomicRegulons

This is used to specify a set of atomic regulons that are to be projected. The first two columns of the table must contain

-e Effectors

This is used to suggest effectors of expression. The first column must contain an atomic regulon number. The second to last column must contain a code indicting the type of regulation (-,+,+-, or u). The last column contains the effector. Each line may be thought of as stating that the effector activates or represses expression of the atomic regulon.

-g TargetGenome

This specifies the genome to which the projection is made

-m ModelDir

The program creates a directory (ModelDir) that will contain

    atomic.regulons - a projection of the atomic regulons expressed
                      as a 2 column table [Id,Gene-in-atomic-regulon]

    effectors       - a projection of the effetors expressed as 3 columns


The output is the ModelDir containing two files, one specifying the atomic regulons, and one the effectors. We allow singleton atomic regulons. They should be thought of as a means of reflecting the impact of an effector on a single gene (although some singletons have no associated effectors).