Secondary structural entropy in RNA switch (Riboswitch) identification

Manzourolajdad, Amirhossein; Arnold, Jonathan

doi:10.1186/s12859-015-0523-2

BMC Bioinformatics

Table 23 Top classification hits in B. subtilis uracil-comp. constrained

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	4134175	4134331	reverse	BSU40230	yydA	-182	0.3439	79	yydB	BSU40220	0.931
2	3714883	3715039	forward	BSU36030	ywrK	-859	0.3949	2277	cotG	BSU36070	0.922
3	3866327	3866483	reverse	BSU37690	ywfG	-1881	0.3503	79	eutD	BSU37660	0.903
4	681153	681309	forward	BSU06260	ydjN	-201	0.3885	5731	yeaB	BSU06320	0.899
5	1680274	1680430	forward	BSU16080	ylqH	63	0.3822	79	sucC	BSU16090	0.897
6	2316268	2316424	reverse	BSU22040	ypbQ	-99	0.363	236	ypbR	BSU22030	0.896
7	688027	688183	forward	BSU06320	yeaB	-114	0.3885	79	yeaC	BSU06330	0.893
8	243578	243734	forward	BSU02170	ybfB	-5370	0.363	236	purT	BSU02230	0.89
9	984466	984622	reverse	BSU09120	yhcK	-1189	0.3885	79	cspB	BSU09100	0.889
10	3421066	3421222	reverse	BSU33340	sspJ	-320	0.3312	79	lysP	BSU33330	0.885
11	1493630	1493786	forward	BSU14230	ykuV	-230	0.3503	79	rok	BSU14240	0.879
12	2531945	2532101	forward	BSU24210	yqiG	-14308	0.3439	9028	yqhQ	BSU24490	0.879
13	300673	300829	forward	BSU02770	yccK	-1196	0.3822	79	ycdB	BSU02790	0.875
14	4139318	4139474	forward	BSU40240	yycS	-3475	0.3567	864	rapG	BSU40300	0.865
15	3681213	3681369	forward	BSU35670	gtaB	-14627	0.363	79	tagA	BSU35750	0.864
16	3671690	3671846	reverse	BSU35700	tagH	-1795	0.3694	393	ggaA	BSU35690	0.859
17	191850	192006	forward	BSU01590	ybaS	-12186	0.3057	2277	trnSL-Glu2	BSU_tRNA_75	0.856
18	20723	20879	forward	BSU00120	yaaE	-86	0.3185	79	serS	BSU00130	0.856
19	2691445	2691601	reverse	BSU26240	yqaO	-1121	0.3439	79	yqaQ	BSU26220	0.852
20	3158851	3159007	reverse	BSU30890	ytxO	-328	0.363	3376	ytdA	BSU30850	0.852
21	1958206	1958362	forward	BSU18190	yngC	-9863	0.3949	44353	iseA	BSU18380	0.852
22	557716	557872	forward	BSU05100	yddT	-188	0.3503	79	ydzN	BSU05109	0.851
23	3907629	3907785	reverse	BSU38100	ywcH	-2594	0.3567	393	ywcI	BSU38080	0.851
24	1926523	1926679	forward	BSU17950	yneJ	-1482	0.3949	79	citB	BSU18000	0.851
25	1017271	1017427	forward	BSU09400	spoVR	-139	0.363	1649	lytE	BSU09420	0.85
26	2769617	2769773	reverse	BSU27160	cypB	-4194	0.3185	1021	yrhP	BSU27100	0.849
27	2739991	2740147	reverse	BSU26830	yrpE	-1287	0.3694	3533	aadK	BSU26790	0.849
28	644384	644540	forward	BSU05940	gcp	-7	0.3694	2120	moaC	BSU05960	0.848
29	2203622	2203778	forward	BSU20580	yoqM	-7279	0.363	79	yopS	BSU20780	0.847
30	3014345	3014501	reverse	BSU29460	moaB	-90	0.3694	79	argG	BSU29450	0.847
31	749147	749303	forward	BSU06780	yeeC	-3069	0.363	550	yeeG	BSU06820	0.846
32	665425	665581	forward	BSU06130	ydjC	-677	0.3439	1963	gutB	BSU06150	0.846
33	2106272	2106428	reverse	BSU19360	odhB	-1154	0.3949	79	yocR	BSU19340	0.846
34	226409	226565	forward	BSU02050	ybdO	-82	0.3885	79	ybxG	BSU02060	0.844
35	2106333	2106489	forward	BSU19330	sodF	-1353	0.3885	79	yocS	BSU19350	0.844
36	308175	308331	forward	BSU02840	ycdG	48	0.3503	79	adcA	BSU02850	0.843
37	2678925	2679081	forward	BSU26050	yqdB	-427	0.363	12639	yqaP	BSU26230	0.843
38	3875571	3875727	reverse	BSU37760	rocC	-130	0.3121	79	ywfA	BSU37750	0.843
39	2433680	2433836	reverse	BSU23340	ypuB	-384	0.3885	236	ypzJ	BSU23328	0.843
40	1533806	1533962	forward	BSU14610	pdhD	-445	0.3503	236	ykzW	BSU14629	0.841
41	368137	368293	forward	BSU03360	yciC	-802	0.3312	1021	yckC	BSU03390	0.841
42	447000	447156	forward	BSU03930	gdh	-792	0.3121	2120	ycnL	BSU03970	0.84
43	2065804	2065960	forward	BSU18960	yozM	-348	0.3758	8557	yobN	BSU19020	0.839
44	45296	45452	reverse	BSU01550	gerD	-113140	0.3822	236	abrB	BSU00370	0.837
45	2048779	2048935	reverse	BSU18810	yobA	-1092	0.363	550	yoaZ	BSU18790	0.836
46	3153718	3153874	reverse	BSU30850	ytdA	-938	0.3439	79	menF	BSU30830	0.836
47	3388260	3388416	reverse	BSU33040	fumC	-685	0.3312	393	yuzO	BSU33029	0.834
48	205252	205408	forward	BSU01820	adaB	-283	0.3248	79	ndhF	BSU01830	0.834
49	469269	469425	forward	BSU04160	mtlR	24	0.3121	79	ydaB	BSU04170	0.834
50	1868460	1868616	forward	BSU17360	ymzA	-7	0.3885	79	nrdI	BSU17370	0.834
51	3746069	3746225	forward	BSU36380	rapD	-577	0.3822	2905	ywoH	BSU36440	0.833
52	3467327	3467483	reverse	BSU33800	opuCD	-140	0.3376	79	sdpR	BSU33790	0.832
53	1903262	1903418	reverse	BSU17690	yncM	-170	0.3822	1963	cotU	BSU17670	0.831
54	1017114	1017270	forward	BSU09400	spoVR	18	0.3376	1806	lytE	BSU09420	0.831
55	2709577	2709733	reverse	BSU26490	yrkJ	-346	0.3503	236	yrkK	BSU26480	0.829
56	955738	955894	forward	BSU08780	ygaJ	-74	0.3822	79	thiC	BSU08790	0.828
57	1283149	1283305	forward	BSU12100	yjeA	-539	0.3758	236	yjfC	BSU12130	0.827
58	3988764	3988920	reverse	BSU38860	galE	-1105	0.293	79	yxkD	BSU38840	0.825
59	200120	200276	forward	BSU01770	glmM	-198	0.2611	79	glmS	BSU01780	0.825
60	2186812	2186968	reverse	BSU20420	yorD	-94	0.2611	79	yorE	BSU20410	0.825
61	2926840	2926996	reverse	BSU28630	pheT	-89	0.3185	1021	yshA	BSU28610	0.823
62	2054401	2054557	reverse	BSU18840	xynA	-119	0.3822	550	pps	BSU18830	0.822
63	610963	611119	reverse	BSU05660	ydgI	-1149	0.3121	2277	dinB	BSU05630	0.822
64	3457144	3457300	reverse	BSU33700	opuBD	-2583	0.3185	707	yvzC	BSU33650	0.821
65	736435	736591	reverse	BSU06740	yefB	-2481	0.3376	3690	yerO	BSU06700	0.82
66	2061478	2061634	reverse	BSU18930	yobH	-1953	0.3439	864	yozJ	BSU18900	0.82
67	3268477	3268633	forward	BSU31810	yuzE	-4174	0.3949	8400	yukF	BSU31920	0.82
68	3107044	3107200	forward	BSU30340	ytvA	30	0.2675	1492	yttA	BSU30360	0.82
69	2262616	2262772	reverse	BSU21440	bdbB	-2530	0.3885	15151	youB	BSU21329	0.819
70	4118717	4118873	reverse	BSU40110	bglA	-2370	0.3758	5574	glxK	BSU40040	0.818
71	4204755	4204911	reverse	BSU40960	parB	-722	0.3949	393	yyaD	BSU40940	0.818
72	252357	252513	forward	BSU02320	ybfP	36	0.3822	79	ybfQ	BSU02330	0.818
73	3648264	3648420	reverse	BSU35530	tagO	-311	0.363	1806	degS	BSU35500	0.818
74	850053	850209	forward	BSU07750	yflA	-3789	0.3694	236	treP	BSU07800	0.817
75	255279	255435	forward	BSU02330	ybfQ	-1718	0.2994	2434	ybgA	BSU02370	0.816
76	1541729	1541885	forward	BSU14680	ykzC	-2958	0.3376	79	ylaA	BSU14710	0.816
77	909862	910018	forward	BSU08330	yfiN	-658	0.3503	79	estB	BSU08350	0.816
78	4109617	4109773	reverse	BSU40030	yxaB	-1253	0.3885	79	yxaD	BSU40010	0.813
79	3252983	3253139	forward	BSU31660	mrpG	-538	0.3949	4632	yuzC	BSU31730	0.811
80	4066294	4066450	reverse	BSU39600	yxeC	-234	0.3567	864	yxeF	BSU39570	0.81
81	1923077	1923233	forward	BSU17910	yneF	-231	0.3248	79	ccdA	BSU17930	0.809
82	1540787	1540943	forward	BSU14680	ykzC	-2016	0.3503	1021	ylaA	BSU14710	0.809
83	3665472	3665628	forward	BSU35650	lytR	-1192	0.3376	79	gtaB	BSU35670	0.808
84	1679031	1679187	reverse	BSU17060	ymzD	-101508	0.3503	7458	ylqB	BSU15960	0.808
85	2698717	2698873	reverse	BSU26360	yqaD	-714	0.363	79	yqaF	BSU26340	0.808
86	3604725	3604881	reverse	BSU35100	yvlD	-1958	0.363	236	yvmC	BSU35070	0.808
87	3354671	3354827	forward	BSU32650	yurS	-105	0.3057	17820	yuzL	BSU32849	0.807
88	3052234	3052390	forward	BSU29710	acuC	-9600	0.3503	2434	ytoQ	BSU29850	0.806
89	188867	189023	forward	BSU01590	ybaS	-9203	0.3185	5260	trnSL-Glu2	BSU_tRNA_75	0.806
90	245389	245545	reverse	BSU02340	gltP	-8050	0.363	1806	ybfI	BSU02220	0.805
91	1445373	1445529	reverse	BSU13810	ykvS	-2210	0.3439	2748	ykvN	BSU13760	0.804
92	2249114	2249270	reverse	BSU21440	bdbB	-16032	0.3439	1649	youB	BSU21329	0.803
93	3918262	3918418	reverse	BSU38190	galT	-752	0.3057	79	qoxA	BSU38170	0.801
94	933760	933916	reverse	BSU08620	yfhP	-618	0.3439	5574	sspK	BSU08550	0.8
95	201248	201404	reverse	BSU01800	alkA	-1220	0.293	7301	ybbK	BSU01720	0.8
96	3684268	3684424	reverse	BSU35780	lytD	-479	0.3439	3376	tagD	BSU35740	0.8
97	2739834	2739990	reverse	BSU26830	yrpE	-1444	0.3439	3376	aadK	BSU26790	0.799
98	2252097	2252253	reverse	BSU21440	bdbB	-13049	0.3949	4632	youB	BSU21329	0.798
99	1601271	1601427	reverse	BSU15640	yloA	-34781	0.3503	24100	ylbP	BSU15100	0.797
100	2111609	2111765	reverse	BSU19380	yojO	-149	0.3439	79	sucA	BSU19370	0.796

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. Uracil composition constrained to that of the range of known riboswitches in B. subtilis (between 0.2484 and 0.40127). 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.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com