Secondary structural entropy in RNA switch (Riboswitch) identification

Manzourolajdad, Amirhossein; Arnold, Jonathan

doi:10.1186/s12859-015-0523-2

BMC Bioinformatics

Table 27 Top classification hits in E. coli

From: Secondary structural entropy in RNA switch (Riboswitch) identification

R	Start	End	Strand	Upstream operon	Dist. to upstream	Uracil	Dist. to downstream	Downstream operon	Probability
1	384006	384105	forward	insC-1,insCD-1,insD-1	-2154	0.52	402	tauA,tauB,tauC,tauD	0.942
2	237185	237284	forward	aspV	-129	0.47	102	yafT	0.934
3	2777119	2777218	forward	yfjX,yfjY,yfjZ,ypjF,ypjJ	-1266	0.38	7252	ygaQ_1,ygaQ_2	0.925
4	2304856	2304955	forward	eco	-2392	0.45	6202	micF	0.923
5	83968	84067	forward	setA,sgrS,sgrT	-5120	0.49	352	leuO	0.92
6	2902496	2902595	reverse	queE	-224	0.48	4249	ygcW	0.918
7	294815	294914	forward	yagJ	-3311	0.43	7352	yagU	0.914
8	4554566	4554665	forward	uxuR	-1145	0.48	402	iraD	0.913
9	405479	405578	forward	yaiI	16	0.45	102	aroL,aroM,yaiA	0.908
10	4570237	4570336	forward	yjiS	-250	0.38	152	yjiT	0.906
11	754000	754099	forward	nei,ybgI,ybgJ,ybgK,ybgL	-8002	0.4	352	sdhA¹	0.905
12	2054653	2054752	reverse	asnW	-1349	0.44	3349	yeeL_1,yeeL_2	0.905
13	2202241	2202340	reverse	yehS	-7458	0.44	10099	mrp	0.903
14	330995	331094	forward	betT	-226	0.52	552	yahA	0.9
15	3183291	3183390	reverse	glgS	-6421	0.44	599	ribB,sroG	0.9
16	384056	384155	forward	insC-1,insCD-1,insD-1	-2204	0.43	352	tauA,tauB,tauC,tauD	0.898
17	4570187	4570286	forward	yjiS	-200	0.42	202	yjiT	0.898
18	557285	557384	forward	cysS	-2017	0.35	102	sfmA	0.894
19	3190062	3190161	reverse	sibD	-2632	0.37	149	glgS	0.893
20	1543575	1543674	forward	nhoA	-10633	0.45	1802	fdnG,fdnH,fdnI	0.89
21	2190295	2190394	reverse	yehE	-193	0.46	99	yehA,yehB,yehC,yehD	0.89
22	3181507	3181606	reverse	ribB,sroG	-279	0.43	1099	ygiD	0.89
23	3834703	3834802	reverse	nlpA	-2446	0.37	799	yicI,yicJ	0.889
24	1753166	1753265	reverse	ynhG	-2530	0.45	49	ydhZ	0.888
25	819916	820015	forward	ybhL	-56	0.41	52	ybhM	0.887
26	2901746	2901845	reverse	queE	-974	0.51	3499	ygcW	0.887
27	651208	651307	forward	ybdR	-8610	0.49	202	dpiA,dpiB	0.886
28	584973	585072	forward	appY	-1271	0.57	9802	cusA,cusB,cusC,cusF	0.886
29	2362398	2362497	reverse	ais	-593	0.48	149	yfaZ	0.886
30	1596214	1596313	forward	osmC	-41085	0.39	3252	lsrA,lsrB,lsrC,lsrD,lsrF,lsrG,tam	0.882
31	522335	522434	forward	ybbA,ybbP	-232	0.39	102	rhsD,ybbC,ybbD,ylbH	0.881
32	3490420	3490519	reverse	php,yhfS,yhfT,yhfU,yhfW,yhfX	-12488	0.39	149	ppiA	0.88
33	1986023	1986122	reverse	yecH	-1203	0.45	49	isrB	0.879
34	3217299	3217398	reverse	ygjH	-1589	0.42	249	aer	0.878
35	2714626	2714725	forward	eamB	-545	0.45	102	ung	0.877
36	3984255	3984354	forward	aslB	-1990	0.42	152	glmZ	0.877
37	2651611	2651710	reverse	sseB	-519	0.5	99	C0614	0.877
38	4516300	4516399	forward	insO-2,yjhV,yjhW	-8095	0.39	202	insA-7	0.876
39	3886253	3886352	reverse	purP	-6993	0.31	4549	dnaA,dnaN,recF	0.876
40	1577414	1577513	forward	osmC	-22285	0.41	22052	lsrA,lsrB,lsrC,lsrD,lsrF,lsrG,tam	0.875
41	776349	776448	reverse	zitB	-6707	0.39	11299	mngR	0.874
42	1543625	1543724	forward	nhoA	-10683	0.46	1752	fdnG,fdnH,fdnI	0.871
43	29201	29300	forward	dapB	43	0.49	402	carA,carB	0.871
44	1542975	1543074	forward	nhoA	-10033	0.39	2402	fdnG,fdnH,fdnI	0.871
45	3768179	3768278	reverse	yibH,yibI	-38	0.41	8249	yibF	0.871
46	3631114	3631213	forward	yhhI	-7528	0.4	1702	yhiM	0.87
47	2166486	2166585	forward	cyaR	-1213	0.41	202	yegS	0.87
48	4578972	4579071	forward	symR	-989	0.38	5952	mrr	0.869
49	522235	522334	forward	ybbA,ybbP	-132	0.39	202	rhsD,ybbC,ybbD,ylbH	0.869
50	2383795	2383894	reverse	yfbN	-1888	0.48	99	yfbK	0.869
51	4577258	4577357	forward	yjiV	-2331	0.36	552	symR	0.868
52	153855	153954	forward	yadD	-5936	0.37	8202	hrpB	0.868
53	3665704	3665803	reverse	yhjA	-61	0.42	149	gadA,gadW,gadX	0.868
54	3651672	3651771	reverse	hdeA,hdeB,yhiD	-1557	0.45	499	insH-11	0.868
55	4619642	4619741	forward	deoA,deoB,deoC,deoD	32	0.38	102	yjjJ	0.867
56	1645875	1645974	reverse	ynfP	-4828	0.45	49	dicC,ydfW,ydfX	0.867
57	4554516	4554615	forward	uxuR	-1095	0.42	452	iraD	0.866
58	4539860	4539959	forward	fimB	-229	0.41	152	fimE	0.866
59	1588711	1588810	reverse	hipA,hipB	-118	0.4	199	yneL	0.866
60	3181557	3181656	reverse	ribB,sroG	-229	0.33	1149	ygiD	0.865
61	269657	269756	reverse	insH-1	-3619	0.45	299	perR	0.864
62	3925028	3925127	forward	cbrB,cbrC	-28347	0.47	102	asnA	0.863
63	4538580	4538679	forward	yjhR	-4477	0.43	352	fimB	0.863
64	4077095	4077194	reverse	fdhE,fdoG,fdoH,fdoI	-1178	0.39	5549	yihS,yihT,yihU	0.863
65	1210379	1210478	reverse	iraM	-475	0.42	1549	stfE,tfaE	0.862
66	4213351	4213450	forward	metA	-70	0.37	102	aceA,aceB,aceK	0.861
67	578853	578952	forward	essD,rrrD,rzpD	-1013	0.49	202	ybcW	0.861
68	3755951	3756050	reverse	selA,selB	-40	0.33	149	yiaY	0.861
69	924768	924867	forward	clpA	44	0.36	7002	lrp	0.86
70	2520650	2520749	reverse	xapA,xapB	-52	0.42	199	xapR	0.86
71	582454	582553	forward	tfaX	-122	0.44	402	appY	0.859
72	1049984	1050083	forward	insA-4,insAB-4,insB-4	-182	0.38	652	cspG	0.859
73	3767704	3767803	forward	yibG	-994	0.36	2552	mtlA,mtlD,mtlR	0.859
74	2383745	2383844	reverse	yfbN	-1938	0.45	49	yfbK	0.859
75	1005025	1005124	forward	pyrD	25	0.46	102	zapC	0.858
76	157105	157204	forward	yadD	-9186	0.34	4952	hrpB	0.858
77	1669567	1669666	reverse	mdtI,mdtJ	-1228	0.46	1999	ynfL	0.858
78	3800263	3800362	forward	rfaD,waaC,waaF,waaL	-3984	0.35	6252	coaD,waaA	0.856
79	2784960	2785059	reverse	ygaU	-9350	0.41	1149	ileY	0.856
80	2468130	2468229	reverse	yfdK,yfdL,yfdM,yfdN,yfdO	-920	0.49	5149	mlaA	0.855
81	2991883	2991982	reverse	ygeK,ygeL	-550	0.39	3549	yqeK	0.855
82	2859337	2859436	reverse	nlpD,rpoS	-5195	0.42	99	ygbI	0.855
83	3490370	3490469	reverse	php,yhfS,yhfT,yhfU,yhfW,yhfX	-12538	0.32	99	ppiA	0.854
84	4220501	4220600	forward	aceA,aceB,aceK	-2097	0.37	1302	metH	0.853
85	715871	715970	reverse	potE,speF	-249	0.37	99	ybfG,ybfH	0.853
86	2461957	2462056	reverse	mlaA	-268	0.45	3049	yfcZ	0.852
87	2876502	2876601	reverse	cas1,cas2,casA,casB,casC,casD,casE	-40	0.34	2199	cysC,cysD,cysN	0.851
88	4084875	4084974	forward	fdhD	46	0.42	102	yiiG	0.85
89	4535630	4535729	forward	yjhR	-1527	0.31	3302	fimB	0.849
90	1635392	1635491	reverse	gnsB	-192	0.42	1049	nohA,tfaQ,ydfN	0.849
91	3497220	3497319	reverse	php,yhfS,yhfT,yhfU,yhfW,yhfX	-5688	0.33	6949	ppiA	0.849
92	3266938	3267037	reverse	garK,garL,garP,garR,rnpB	-1251	0.35	1899	tdcA,tdcB,tdcC,tdcD,tdcE,tdcF,tdcG	0.848
93	2267568	2267667	reverse	yejG	-8298	0.34	4299	yeiW	0.848
94	3580990	3581089	reverse	ggt	-2065	0.4	1999	ryhB	0.848
95	1811219	1811318	reverse	cedA	-177	0.5	99	ydjO	0.845
96	583210	583309	reverse	envY,ompT	-644	0.4	1299	ybcY	0.845
97	3576850	3576949	reverse	yhhW	-74	0.33	149	gntK,gntR,gntU	0.844
98	3266488	3266587	reverse	garK,garL,garP,garR,rnpB	-1701	0.43	1449	tdcA,tdcB,tdcC,tdcD,tdcE,tdcF,tdcG	0.843
99	2055603	2055702	reverse	asnW	-399	0.33	4299	yeeL_1,yeeL_2	0.843
100	2739273	2739372	reverse	rimM,rplS,rpsP,trmD	-2883	0.3	149	aroF,tyrA	0.842

Top 50 hits of the forward and reverse strands of the E. coli intergenic regions using 50 nt-overlap 100 nt window and under the LMFEGCRND model. The ranking of each hit is denoted in column R. 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.
¹Table 27: Complete list of genes in this operon is sdhA,sdhB,sdhC,sdhD,sucA,sucB,sucC,sucD.

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