Secondary structural entropy in RNA switch (Riboswitch) identification

Manzourolajdad, Amirhossein; Arnold, Jonathan

doi:10.1186/s12859-015-0523-2

BMC Bioinformatics

Table 22 Top classification hits in B. subtilis

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

R	Start	End	Strand	Upstream operon	Upstream gene	Dist. to upstream	Uracil	Dist. to downstream	Downstream gene	Downstream operon	Probability
1	3717569	3717725	reverse	BSU36100	ywrD	-1486	0.4076	550	cotH	BSU36060	0.943
2	3717412	3717568	reverse	BSU36100	ywrD	-1643	0.4076	393	cotH	BSU36060	0.935
3	4134175	4134331	reverse	BSU40230	yydA	-182	0.3439	79	yydB	BSU40220	0.931
4	3714883	3715039	forward	BSU36030	ywrK	-859	0.3949	2277	cotG	BSU36070	0.922
5	748990	749146	forward	BSU06780	yeeC	-2912	0.414	707	yeeG	BSU06820	0.919
6	3666640	3666796	reverse	BSU35680	ggaB	-490	0.4968	1335	mnaA	BSU35660	0.908
7	3866327	3866483	reverse	BSU37690	ywfG	-1881	0.3503	79	eutD	BSU37660	0.903
8	681153	681309	forward	BSU06260	ydjN	-201	0.3885	5731	yeaB	BSU06320	0.899
9	2987548	2987704	reverse	BSU29200	accA	-104	0.4268	79	pfkA	BSU29190	0.898
10	1680274	1680430	forward	BSU16080	ylqH	63	0.3822	79	sucC	BSU16090	0.897
11	2730227	2730383	reverse	BSU26730	yrdF	-254	0.4204	79	azlB	BSU26720	0.896
12	2316268	2316424	reverse	BSU22040	ypbQ	-99	0.363	236	ypbR	BSU22030	0.896
13	2219985	2220141	forward	BSU20929	yoyI	-6828	0.4204	2277	yonP	BSU21030	0.896
14	688027	688183	forward	BSU06320	yeaB	-114	0.3885	79	yeaC	BSU06330	0.893
15	243578	243734	forward	BSU02170	ybfB	-5370	0.363	236	purT	BSU02230	0.89
16	984466	984622	reverse	BSU09120	yhcK	-1189	0.3885	79	cspB	BSU09100	0.889
17	2376780	2376936	forward	BSU22510	ypjC	-15199	0.4395	16564	ypzI	BSU22869	0.888
18	748205	748361	forward	BSU06780	yeeC	-2127	0.4395	1492	yeeG	BSU06820	0.886
19	3421066	3421222	reverse	BSU33340	sspJ	-320	0.3312	79	lysP	BSU33330	0.885
20	2093235	2093391	forward	BSU19200	desR	-852	0.4331	4789	yoyB	BSU19259	0.88
21	3941212	3941368	reverse	BSU38430	gspA	-3269	0.4777	1649	ywbA	BSU38390	0.879
22	1493630	1493786	forward	BSU14230	ykuV	-230	0.3503	79	rok	BSU14240	0.879
23	2531945	2532101	forward	BSU24210	yqiG	-14308	0.3439	9028	yqhQ	BSU24490	0.879
24	746478	746634	forward	BSU06780	yeeC	-400	0.5095	3219	yeeG	BSU06820	0.878
25	2096100	2096256	reverse	BSU19230	yocJ	-171	0.4268	393	yocI	BSU19220	0.877
26	300673	300829	forward	BSU02770	yccK	-1196	0.3822	79	ycdB	BSU02790	0.875
27	3373963	3374119	reverse	BSU32890	yusQ	-2575	0.4076	393	fadM	BSU32850	0.874
28	3686143	3686299	forward	BSU35770	tagC	-1298	0.4586	2591	gerBA	BSU35800	0.87
29	1335487	1335643	reverse	BSU12820	spoIISB	-12876	0.5032	13895	xre	BSU12510	0.868
30	4139318	4139474	forward	BSU40240	yycS	-3475	0.3567	864	rapG	BSU40300	0.865
31	1268672	1268828	forward	BSU11970	yjcS	-1	0.4458	79	yjdA	BSU11980	0.865
32	3685829	3685985	forward	BSU35770	tagC	-984	0.414	2905	gerBA	BSU35800	0.865
33	3681213	3681369	forward	BSU35670	gtaB	-14627	0.363	79	tagA	BSU35750	0.864
34	1122705	1122861	forward	BSU10490	sipV	55	0.4013	79	yhjG	BSU10500	0.86
35	3671690	3671846	reverse	BSU35700	tagH	-1795	0.3694	393	ggaA	BSU35690	0.859
36	2160701	2160857	forward	BSU20000	yosU	-1938	0.4395	9028	yosA	BSU20190	0.859
37	1097850	1098006	reverse	BSU10230	yhfH	-191	0.465	79	gltT	BSU10220	0.858
38	1467020	1467176	forward	BSU13960	ykwC	-342	0.414	707	pbpH	BSU13980	0.857
39	191850	192006	forward	BSU01590	ybaS	-12186	0.3057	2277	trnSL-Glu2	BSU_tRNA_75	0.856
40	20723	20879	forward	BSU00120	yaaE	-86	0.3185	79	serS	BSU00130	0.856
41	2691445	2691601	reverse	BSU26240	yqaO	-1121	0.3439	79	yqaQ	BSU26220	0.852
42	3158851	3159007	reverse	BSU30890	ytxO	-328	0.363	3376	ytdA	BSU30850	0.852
43	1958206	1958362	forward	BSU18190	yngC	-9863	0.3949	44353	iseA	BSU18380	0.852
44	557716	557872	forward	BSU05100	yddT	-188	0.3503	79	ydzN	BSU05109	0.851
45	3907629	3907785	reverse	BSU38100	ywcH	-2594	0.3567	393	ywcI	BSU38080	0.851
46	1926523	1926679	forward	BSU17950	yneJ	-1482	0.3949	79	citB	BSU18000	0.851
47	1017271	1017427	forward	BSU09400	spoVR	-139	0.363	1649	lytE	BSU09420	0.85
48	1493595	1493751	reverse	BSU14250	yknT	-729	0.4522	1649	ykuT	BSU14210	0.85
49	2477743	2477899	forward	BSU23830	yqjL	66	0.4076	1335	zwf	BSU23850	0.849
50	2769617	2769773	reverse	BSU27160	cypB	-4194	0.3185	1021	yrhP	BSU27100	0.849
51	2739991	2740147	reverse	BSU26830	yrpE	-1287	0.3694	3533	aadK	BSU26790	0.849
52	644384	644540	forward	BSU05940	gcp	-7	0.3694	2120	moaC	BSU05960	0.848
53	4039599	4039755	forward	BSU39100	yxiO	-23552	0.4713	1806	hutP	BSU39340	0.847
54	2203622	2203778	forward	BSU20580	yoqM	-7279	0.363	79	yopS	BSU20780	0.847
55	3014345	3014501	reverse	BSU29460	moaB	-90	0.3694	79	argG	BSU29450	0.847
56	749147	749303	forward	BSU06780	yeeC	-3069	0.363	550	yeeG	BSU06820	0.846
57	665425	665581	forward	BSU06130	ydjC	-677	0.3439	1963	gutB	BSU06150	0.846
58	2106272	2106428	reverse	BSU19360	odhB	-1154	0.3949	79	yocR	BSU19340	0.846
59	226409	226565	forward	BSU02050	ybdO	-82	0.3885	79	ybxG	BSU02060	0.844
60	2106333	2106489	forward	BSU19330	sodF	-1353	0.3885	79	yocS	BSU19350	0.844
61	308175	308331	forward	BSU02840	ycdG	48	0.3503	79	adcA	BSU02850	0.843
62	2678925	2679081	forward	BSU26050	yqdB	-427	0.363	12639	yqaP	BSU26230	0.843
63	3875571	3875727	reverse	BSU37760	rocC	-130	0.3121	79	ywfA	BSU37750	0.843
64	2433680	2433836	reverse	BSU23340	ypuB	-384	0.3885	236	ypzJ	BSU23328	0.843
65	2879134	2879290	reverse	BSU28190	engB	-669	0.4013	79	hemA	BSU28170	0.842
66	1533806	1533962	forward	BSU14610	pdhD	-445	0.3503	236	ykzW	BSU14629	0.841
67	368137	368293	forward	BSU03360	yciC	-802	0.3312	1021	yckC	BSU03390	0.841
68	447000	447156	forward	BSU03930	gdh	-792	0.3121	2120	ycnL	BSU03970	0.84
69	3726630	3726786	forward	BSU36160	ywqM	-2216	0.4331	7144	ywqB	BSU36270	0.84
70	543132	543288	reverse	BSU05000	yddK	-2955	0.4904	11697	immR	BSU04820	0.84
71	3268320	3268476	forward	BSU31810	yuzE	-4017	0.4522	8557	yukF	BSU31920	0.84
72	2065804	2065960	forward	BSU18960	yozM	-348	0.3758	8557	yobN	BSU19020	0.839
73	45296	45452	reverse	BSU01550	gerD	-113140	0.3822	236	abrB	BSU00370	0.837
74	2048779	2048935	reverse	BSU18810	yobA	-1092	0.363	550	yoaZ	BSU18790	0.836
75	3153718	3153874	reverse	BSU30850	ytdA	-938	0.3439	79	menF	BSU30830	0.836
76	3388260	3388416	reverse	BSU33040	fumC	-685	0.3312	393	yuzO	BSU33029	0.834
77	205252	205408	forward	BSU01820	adaB	-283	0.3248	79	ndhF	BSU01830	0.834
78	469269	469425	forward	BSU04160	mtlR	24	0.3121	79	ydaB	BSU04170	0.834
79	1868460	1868616	forward	BSU17360	ymzA	-7	0.3885	79	nrdI	BSU17370	0.834
80	3746069	3746225	forward	BSU36380	rapD	-577	0.3822	2905	ywoH	BSU36440	0.833
81	3467327	3467483	reverse	BSU33800	opuCD	-140	0.3376	79	sdpR	BSU33790	0.832
82	1264932	1265088	reverse	BSU11990	yjdB	-4722	0.5223	79	yjcM	BSU11910	0.832
83	1903262	1903418	reverse	BSU17690	yncM	-170	0.3822	1963	cotU	BSU17670	0.831
84	4204441	4204597	reverse	BSU40960	parB	-1036	0.414	79	yyaD	BSU40940	0.831
85	1017114	1017270	forward	BSU09400	spoVR	18	0.3376	1806	lytE	BSU09420	0.831
86	2709577	2709733	reverse	BSU26490	yrkJ	-346	0.3503	236	yrkK	BSU26480	0.829
87	955738	955894	forward	BSU08780	ygaJ	-74	0.3822	79	thiC	BSU08790	0.828
88	554386	554542	reverse	BSU05130	ydeB	-5686	0.4395	1963	lrpB	BSU05060	0.828
89	3988764	3988920	reverse	BSU38860	galE	-1105	0.293	79	yxkD	BSU38840	0.825
90	2186812	2186968	reverse	BSU20420	yorD	-94	0.2611	79	yorE	BSU20410	0.825
91	2926840	2926996	reverse	BSU28630	pheT	-89	0.3185	1021	yshA	BSU28610	0.823
92	2054401	2054557	reverse	BSU18840	xynA	-119	0.3822	550	pps	BSU18830	0.822
93	610963	611119	reverse	BSU05660	ydgI	-1149	0.3121	2277	dinB	BSU05630	0.822
94	3457144	3457300	reverse	BSU33700	opuBD	-2583	0.3185	707	yvzC	BSU33650	0.821
95	736435	736591	reverse	BSU06740	yefB	-2481	0.3376	3690	yerO	BSU06700	0.82
96	2061478	2061634	reverse	BSU18930	yobH	-1953	0.3439	864	yozJ	BSU18900	0.82
97	2262616	2262772	reverse	BSU21440	bdbB	-2530	0.3885	15151	youB	BSU21329	0.819
98	4118717	4118873	reverse	BSU40110	bglA	-2370	0.3758	5574	glxK	BSU40040	0.818
99	4204755	4204911	reverse	BSU40960	parB	-722	0.3949	393	yyaD	BSU40940	0.818
100	3648264	3648420	reverse	BSU35530	tagO	-311	0.363	1806	degS	BSU35500	0.818

Top 50 hits of the forward and reverse strands of the B. subtilis intergenic regions using no-overlap 157 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.
Interesting hits are shown in bold.

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ISSN: 1471-2105

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