Description
The MotifLabModule format is the default format for modules used by
MotifLab, and it is a variation of
the
MotifLabMotif format.
A file in MotifLabModule format must start with a header line
reading "
#MotifLabModule" which serves to identify the
format, and this is followed by a description of the modules (and
optionally also the single motifs involved in these modules).
Each new module is introduced with the line:
#ModuleID = <unique identifier>
This is followed by a list of the motifs involved in the
module:
Motifs = <comma-separated list of "module motif" names>
Note that the "module motif" names in the mentioned list are not single motif
identifiers referencing
Motif objects, but rather descriptive motif names
that are internal to the module (the "module motif" names must be unique within the module).
Each such "module motif" can be represented by multiple single motif
objects, as described by lines in the following
format:
Motif(<module motif>) = <list of Motif identifiers>
Additional constraints regarding the motifs within the module can also be
specified, for example the maximum length of the module:
MaxLength = <maximum number of base pairs the module can span>
Whether the motifs in the module must appear in the order they are listed in
the "Motifs = " line or if they can appear in any order.
Ordered = <true|false>
The module motifs might also have specific orientations relative to each other.
Orientation(<module motif>) = <Direct|Reverse>
Or constraints on the distance between pairs of consecutive motifs in ordered
modules.
Distance(<module motif 1>,<module motif 2>) =
[<min distance>, <max distance>]
Example:
#MotifLabModule
#
#ModuleID = MOD0001
Motifs = STAT,GATA
Ordered = false
MaxLength = 200
Motif(STAT) = M00225,M00492,M00493,M00494,M00500,M00496
Motif(GATA) = M00351,M00350,M00076,M00203,M00077,M00075,M00347,M00346
#ModuleID = MOD0002
Motifs = SRY,AP1
Ordered = true
MaxLength = 200
Motif(SRY) = M00160,M00148
Motif(AP1) =
M00041,M00172,M00039,M00517,M00040,M00113,M00114,M00174,M00115
Orientation(SRY) = Direct
Orientation(AP1) = Reverse
#ModuleID = MOD0003
Motifs = STAT,ER,MYC
Ordered = true
MaxLength = 200
Motif(STAT) = M00225,M00492,M00493,M00494,M00500,M00496,M00497,M00498
Motif(ER) = M00191
Motif(MYC) = M00055,M00322,M00006,M00005,M00007
Orientation(STAT) = Direct
Orientation(ER) = Reverse
Distance(STAT,ER) = [5,10]
Distance(ER,MYC) = [0,16]