SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

Table 1 Summary of found motifs similar to known SigR SFBSs

*S. coelicolor* consensus: ggaatn₁₈gtt [51]
SIGffRid motif	R	LRT	N_U(1)	%_U(2)	N_U∈μ(3)
in S. coelicolor
ggaatn _16,19 gtt	0.49	54.69	79	0.49	32
gggaan _18,20 cgtt	0.48	42.97	58	0.48	12
in S. avermitilis
ggaatn _17,19 gttg	0.51	30.98	38	0.51
ggaatn _17,18 gttg	0.60	30.59	31	0.60
gaatn _17,18 gttg	0.44	25.36	40	0.45

(1) N_Uis the number of occurrences found in merged sequences
(2) %_Uis the proportion of occurrences found in merged sequences (%_U= N_U/N_G, where N_Gis the number of occurrences found in the whole genome on direct and reverse strand)
(3) N_U∈μis the number of occurrences in merged sequences related to a gene over-expressed in microarray data experiments under oxidative stress conditions, from Paget, personal communication

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