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Table 11 Contrasting predictions: regions known to lack LexA sites

From: Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coliK12 DNA

Gene Consensus/Patser Dyad sweeping
b3020 + sc:13.66 - m:6
brnQ - - - m:2
creA + sc:11.67 - m:6
dinJ + sc:11.52 + m:13
ecpD - - + m:9
hofQ - - - m:4
ilvD - - - m:6
ivbL + sc:13.23 + m:21
metE - - + m:13
metR + sc:9.10 + m:13
minC + sc:12.22 + m:11
pshM - - - m:4
rfaJ - - - m:8
rob - - - m:6
xylE + sc:9.15 + m:11
yafL + sc:15.21 + m:13
ybiA + sc:12.07 + m:16
ybiT - - - m:5
ycgJ + sc:13.42 + m:11
ycgL - - - m:3
yciG - - - m:3
ydbH - - - m:3
ydeJ + sc:9.05 - m:6
yecS + sc:9.89 - m:6
yfiE - - - m:6
yfiK - - - m:6
ygjF - - - m:4
yhiX - - - m:4
yiaO - - - m:2
yigN - - - m:5
yjgN - sc:7.66 + m:10
  1. After experiment, Fernandez De Henestrosa et al. [15] rejected this set of genes in which they had predicted LexA sites using other computational methods. We tested the capacity of dyad sweeping and Patser to also reject these false positives. sc, Score as obtained by Patser; m, maximum number of matching dyads. Note that for both methods, most of the genes here show much smaller scores than genes belonging to the LexA regulon (see Table 10).