Table 2 List of variables, definition of each variable, and the value(s) used during the implementation of MARZ with respect to HB
From: MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding
Variable | Definition | Setting |
|---|---|---|
l n | Gapped n-mer length | l n ≤6 |
μ | Number of nucleotides considered | μ≤6 |
κ | Number of nucleotides ignored | κ≤4 |
l | Length of each potential HB binding sequence | l=7 |
L | Number of aligned HB binding sequences | L=101 |
N | Number of HB ChIP peaks | N=3142 |
l c | Length of each HB ChIP peak | l c =100 |
P | Number of scrambles per ChIP peak | P=100 |