RSAT - Help about random-motif

Author

2008 by Matthieu Defrance

Description

Random motif generator.

Motifs are described as position-specific scoring matrix (PSSM), where each column represents a position within the motif, and each ro a residue (A, C, G or T). The cells contain relative or absolute frequencies depending on the selected options.

The motifs are generated by selecting at random, for each column, one "conserved" residue (the degree of conservation (c) is a value between 0 and 1 specified by the user). The remaining frequencies are equaly distributed between the three remaining residues (f_i=(1-c)/3).

All cell values can be multiplied by a user-specific value (m) and rounded in order to obtain count matrices (with occurrences rather than relative frequencies).

Options

• Width (w): Number of columns of the PSSM.

• Conservation (c): relative frequency of the "conserved" conserved residue of each column.

• Multiplier (m). A number by which each cell value is multiplied.

• Round (Boolean). If true, absolute frequencies are rounded to return integer values.

• Motif number (m). Number of motifs (matrices) to be generated.

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For information, contact Matthieu Defrance