Secondary structural entropy in RNA switch (Riboswitch) identification

BMC Bioinformatics

Table 29 Top entropy hits of E. coli filtered for GC- and uracil-comp

*E. coli*	Start	End	Strand	Upstream operon	Dist. to upstream	MFE	MFE p. Val.	GC	RND	RND p. Val.	Uracil	Dist. to downstream	Downstream operon	Probability
100 nt	4083889	4083988	forward	yiiF	-5848	-38.4	0.0267	0.53	58.6367989	0.0365	0.29	102	fdhD	0.789
100 nt	187962	188061	forward	cdaR	-4293	-36.4	0.0466	0.53	59.0985985	0.0229	0.32	1702	rpsB,tff,tsf	0.776
100 nt	952485	952584	forward	ycaK	-2955	-36.8	0.0419	0.52	58.3203011	0.0494	0.27	3452	ycaP	0.765
100 nt	4115038	4115137	forward	uspD,yiiS	-3245	-37	0.0396	0.53	58.3563995	0.0477	0.33	1452	zapB	0.756
*E. coli*	Start	End	Strand	Upstream operon	Dist. to upstream	MFE	MFE p. Val.	GC	RND	RND p. Val.	Uracil	Dist. to downstream	Downstream operon	Probability
150 nt	2686923	2687072	forward	hmp	-1802	-56.00	-	0.5333	90.7522964	0.0077	0.32000	6827	mltF	0.8671584129
150 nt	2887386	2887535	forward	iap	-11672	-56.40	-	0.5333	89.1240005	-	0.0294	2777	queD	0.8254097700
150 nt	3467187	3467336	forward	gspO¹	-2871	-56.10	-	0.5200	88.5419006	0.0450	0.29333	8402	slyX	0.8172816634
150 nt	3576825	3576974	reverse	yhhW	-74	-55.60	-	0.4800	88.6371994	0.0419	0.30666	149	gntK,gntR,gntU	0.8547886610
150 nt	2195866	2196015	reverse	yehS	-13808	-58.00	-	0.5333	88.6897964	0.0405	0.27333	3749	mrp	0.8320623040

Significant hits of the forward and reverse strands of the E. coli intergenic regions having significantly high RND entropy (p-Val. <0.0500), significantly low (p.Val. <0.050), GC and uracil compositions within the range of those for known riboswitches Threshold values and their corresponding p-values have been calculated separately for each genome-wide test. 50 nt overlap used for 100 nt scan (100090 segments). 175 nt overlap used for 150 nt scan (66414 segments). Distance from Upstream and Downstream operons are the distance from the center of the hit to the stop and start codons of upstream and downstream operons, respectively. Probability denotes the multinomial regression likelihood of being a riboswitch under the LMFEGCRND model. Positions are according to gbU00096.2 version of E. coli and not gbU00096.3 version. Negative values indicate distance to upstream operon. Columns Upsream/Downstream Operon show gene ID within the operon.
¹Table 29: Complete list of genes in this operon is gspC,gspD,gspE,gspF,gspG,gspH,gspI,gspJ,gspK,gspL,gspM,gspO.

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