Description Objects from the Class Slots Author(s) See Also Examples
This object contains contains parameters of GADEM analysis
Objects can be created by calls of the form new("motif_gadem", ...)
.
:Number of non-zero k-mer groups.
:Number of top-ranked trimers for spaced dyads (default: 20).
:Print immediate results on screen [1-yes (default), 0-no].
:Number of top-ranked tetramers for spaced dyads (default: 40).
:Number of top-ranked pentamers for spaced dyads (default: 60).
:Number of genetic algorithm (GA) generations (default: 5).
:GA population size (default: 100).
:P-value cutoff for declaring BINDING SITES (default: 0.0002).
:ln(E-value) cutoff for selecting MOTIFS (default: 0.0).
:Base extension and trimming (1 -yes, 0 -no) (default: 1).
:Minimal number of unspecified nucleotides in spaced dyads (default: 0).
:Maximal number of unspecified nucleotides in spaced dyads (default: 10).
:Use top-scoring sequences for deriving PWMs.
:Number of EM steps (default: 40).
:Fraction of sequences used in EM to obtain PWMs in an unseeded analysis (default: 0.5).
:For -posWt 1 or 3, width of central sequence region with large EM weights for PWM optimization (default: 50).
:GADEM keeps two copies of the input sequences internally.
:Sliding window for comparing pwm similarity (default : 6).
:Number of sets of background sequences (default: 10).
:Weight profile for positions on the sequence.
:Reading user-specified background models.
:File name for the seed PWM, when a seeded approach is used.
:Number of input sequences.
:Mask low-complexity sequences or repeats.
:Maximal number of motifs sought.
Arnaud Droit arnaud.droit@crchuq.ulaval.ca
1 | showClass("parameters")
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