D-ORB

The Overrepresented RNA Blocks

M.J. Dupont, F. Major

D-ORB: A Web Server to Extract Structural Features of Related But Unaligned RNA Sequences

J. Mol. Biol., 435 (2023)

CRISPR RNA direct repeat element (Rfam: RF01315)

Options

Negatives sequences: Random sequences of similar lengths
ORBs positions sequence: Best consensus structure-matching sequence
Motifs: 162,498 motifs on the alphabet ACGURYN

Rfam

D-ORB

Augmented

(.Y.().UA.)
(.C.().GNN.)
(.A.)
(U()A)

100.0
100.0
100.0
100.0

(.Y.().UA.)
(.A.)

% of positive sequence with ORB

Job*

Email*

Sequence(s)*

Obtain

One structure matching the consensus structure ORBs
Several structures containing instances of most discriminative ORBs

Up to structures per sequence

Position offset nucleotides

Job*

Email*

Wildtype sequence*

Mutant sequences

All SNPs
Submit mutant sequences

Use the mutation generator

Deep neural network:

5-fold cross-validation: 99.9 %
(± 0.0299 %)

Decision tree:

5-fold cross-validation: 89.2 %
(± 14.4 %)

D-ORB structure

D-ORB structure decision tree:

5-fold cross-validation: 97.2 %
(± 5.08 %)

of CP000141.1/1929243-1929272

CP000141.1/1929243-1929272

GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC
(.((.(..(.((...))...))....)).)
.........1.........2.........3
123456789012345678901234567890

abstract shape: `()`

					Number of sequences
	Structure	ORBs			(out of 19)	(%)
1		(.Y.().UA.)			17	89.5
>CP000771.1/1024868-1024839 GUUUCAAUCCCUAAUAGGUAUGCUAAAAGC ...(.(...............)....)... >CP000716.1/360504-360533 AUUUCAAUUCCUCCAAGGUAAGGUAAAAAC ...(.(...............)....)... >CP000557.1/317462-317433 GUUUCAAUCUCUCAUAGGUACGAUACAAAC ...(.(...............)....)... >CP000679.1/62025-62054 GUUUCAAUCCCCAAAGGGAAGGCUACAAAC ...(.(...............)....)... >BA000043.1/355427-355398 GUUUCAAUCCCUCAUAGGUACGAUAAAAAC ...(.(...............)....)... >CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC ...(.(...............)....)... >CP000612.1/587612-587583 GUUUCAAUUCCUUAUAGGUAGGCUGAUAAC .(...(...............)......). >CP000879.1/2085036-2085007 GUUUCCAUUCCUUAUAGGUAGGAUAAAAAG ...(.(...............)....)... >CP000679.1/93158-93187 GUUUCAAUCCCCAAAGGGCAGGCUACAAAC ...(.(...............)....)... >CP000141.1/1949543-1949572 GUUUCAAUCCCAGAUUGGUUCGAUUAAAAC ...(.(...............)....)... >AP009389.1/2004616-2004645 GUUUCAAUUCCUCAUAGGCAGGCUAAAAAC ...(.(...............)....)... >CP000679.1/93287-93316 GUUUCAAUCCCCAAAGGGUAGGCUACAAAC ...(.(...............)....)... >AP008230.1/3154402-3154431 GUUUCAAUCCCUCAUAGGUAAGCUAACAAC ...(.(...............)....)... >CP000568.1/717027-716998 GUUUCAAUUCCUCAUAGGUACGAUACAAAC ...(.(...............)....)... >AARF01000280.1/1425-1454 GUUUCAAUUCCUUAUAGGUACGUUAGAAAC ...(..(...............)...)... >CP000673.1/1722241-1722270 GUUUCAAUUCCUUAUAGGUAGUCUAAAAUC ...(.(...............)...).... >CP001336.1/4172990-4173019 AUUUCAAUUCCUUAUAGGUAAGCUAACAAC ...(.(...............).....)..
2		(.Y.().UA.) (.C.().GNN.)			15	78.9
>CP001336.1/4172990-4173019 AUUUCAAUUCCUUAUAGGUAAGCUAACAAC ...(..(.(.(.....)...))...).... >AP008230.1/3154402-3154431 GUUUCAAUCCCUCAUAGGUAAGCUAACAAC ..(.(..(..(.....)...)).....).. >CP000716.1/360504-360533 AUUUCAAUUCCUCCAAGGUAAGGUAAAAAC ...(.(..(.(.....)....))..).... >CP000141.1/1949543-1949572 GUUUCAAUCCCAGAUUGGUUCGAUUAAAAC ...(.(..(.(.....)...))....)... >CP000771.1/1024868-1024839 GUUUCAAUCCCUAAUAGGUAUGCUAAAAGC ...(.(...(.(....)...))....)... >CP000673.1/1722241-1722270 GUUUCAAUUCCUUAUAGGUAGUCUAAAAUC ...(..(.(.(.....)...))...).... >CP000679.1/93158-93187 GUUUCAAUCCCCAAAGGGCAGGCUACAAAC ...(.(..(.(.....)...))....)... >AP009389.1/2004616-2004645 GUUUCAAUUCCUCAUAGGCAGGCUAAAAAC ...(.(..(.(.....)...))....)... >CP000679.1/93287-93316 GUUUCAAUCCCCAAAGGGUAGGCUACAAAC ...(.(..(.(.....)...))....)... >CP000557.1/317462-317433 GUUUCAAUCUCUCAUAGGUACGAUACAAAC ...(...(.(.(....)....))...)... >AARF01000280.1/1425-1454 GUUUCAAUUCCUUAUAGGUACGUUAGAAAC ...(..(.(.(.....)....))...)... >CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC ...(.(..(.(.....)...))....)... >CP000568.1/717027-716998 GUUUCAAUUCCUCAUAGGUACGAUACAAAC ...(.(..(.(.....)...))....)... >CP000679.1/62025-62054 GUUUCAAUCCCCAAAGGGAAGGCUACAAAC ...(.(..(.(.....)...))....)... >BA000043.1/355427-355398 GUUUCAAUCCCUCAUAGGUACGAUAAAAAC ...(.(..(.(.....)...))....)...
3		(.Y.().UA.) (.C.().GNN.) (.A.)			13	68.4
>AP008230.1/3154402-3154431 GUUUCAAUCCCUCAUAGGUAAGCUAACAAC ..(.(..(..((...))...)).....).. >CP000679.1/62025-62054 GUUUCAAUCCCCAAAGGGAAGGCUACAAAC ...(.(..(.((...))...))....)... >AP009389.1/2004616-2004645 GUUUCAAUUCCUCAUAGGCAGGCUAAAAAC ...(.(..(.((...))...))....)... >CP000716.1/360504-360533 AUUUCAAUUCCUCCAAGGUAAGGUAAAAAC ...(.(..(.((...))....))..).... >CP000679.1/93158-93187 GUUUCAAUCCCCAAAGGGCAGGCUACAAAC ...(.(..(.((...))...))....)... >CP000673.1/1722241-1722270 GUUUCAAUUCCUUAUAGGUAGUCUAAAAUC ...(..(.(.((...))...))...).... >AARF01000280.1/1425-1454 GUUUCAAUUCCUUAUAGGUACGUUAGAAAC ...(..(.(.((...))....))...)... >CP000679.1/93287-93316 GUUUCAAUCCCCAAAGGGUAGGCUACAAAC ...(.(..(.((...))...))....)... >CP000557.1/317462-317433 GUUUCAAUCUCUCAUAGGUACGAUACAAAC ...(...(.(.((..))....))...)... >BA000043.1/355427-355398 GUUUCAAUCCCUCAUAGGUACGAUAAAAAC ...(.(..(.((...))...))....)... >CP000568.1/717027-716998 GUUUCAAUUCCUCAUAGGUACGAUACAAAC ...(.(..(.((...))...))....)... >CP000141.1/1949543-1949572 GUUUCAAUCCCAGAUUGGUUCGAUUAAAAC ...(.(..(.((...))...))....)... >CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC ...(.(..(.((...))...))....)...
4		(.Y.().UA.) (.C.().GNN.) (.A.) (U()A)			12	63.2
>CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC (.((.(..(.((...))...))....)).) >AP009389.1/2004616-2004645 GUUUCAAUUCCUCAUAGGCAGGCUAAAAAC (.((.(..(.((...))...))....)).) >CP000679.1/93287-93316 GUUUCAAUCCCCAAAGGGUAGGCUACAAAC (.((.(..(.((...))...))....)).) >CP000568.1/717027-716998 GUUUCAAUUCCUCAUAGGUACGAUACAAAC (.((.(..(.((...))...))....)).) >AARF01000280.1/1425-1454 GUUUCAAUUCCUUAUAGGUACGUUAGAAAC (.((..(.(.((...))....))...)).) >CP000673.1/1722241-1722270 GUUUCAAUUCCUUAUAGGUAGUCUAAAAUC (.((..(.(.((...))...))...)).). >CP000557.1/317462-317433 GUUUCAAUCUCUCAUAGGUACGAUACAAAC (.((...(.(.((..))....))...)).) >CP000716.1/360504-360533 AUUUCAAUUCCUCCAAGGUAAGGUAAAAAC (.((.(..(.((...))....))..)).). >CP000679.1/93158-93187 GUUUCAAUCCCCAAAGGGCAGGCUACAAAC (.((.(..(.((...))...))....)).) >CP000679.1/62025-62054 GUUUCAAUCCCCAAAGGGAAGGCUACAAAC (.((.(..(.((...))...))....)).) >CP000141.1/1949543-1949572 GUUUCAAUCCCAGAUUGGUUCGAUUAAAAC (.((.(..(.((...))...))....)).) >BA000043.1/355427-355398 GUUUCAAUCCCUCAUAGGUACGAUAAAAAC (.((.(..(.((...))...))....)).)

>CP000716.1/360504-360533 AUUUCAAUUCCUCCAAGGUAAGGUAAAAAC ...(.(...............)....)... ...(.(..(.(.....)....))..).... ...(.(..(.((...))....))..).... (.((.(..(.((...))....))..)).). >CP000557.1/317462-317433 GUUUCAAUCUCUCAUAGGUACGAUACAAAC ...(.(...............)....)... ...(...(.(.(....)....))...)... ...(...(.(.((..))....))...)... (.((...(.(.((..))....))...)).) >CP000679.1/62025-62054 GUUUCAAUCCCCAAAGGGAAGGCUACAAAC ...(.(...............)....)... ...(.(..(.(.....)...))....)... ...(.(..(.((...))...))....)... (.((.(..(.((...))...))....)).) >BA000043.1/355427-355398 GUUUCAAUCCCUCAUAGGUACGAUAAAAAC ...(.(...............)....)... ...(.(..(.(.....)...))....)... ...(.(..(.((...))...))....)... (.((.(..(.((...))...))....)).) >CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC ...(.(...............)....)... ...(.(..(.(.....)...))....)... ...(.(..(.((...))...))....)... (.((.(..(.((...))...))....)).) >CP000679.1/93158-93187 GUUUCAAUCCCCAAAGGGCAGGCUACAAAC ...(.(...............)....)... ...(.(..(.(.....)...))....)... ...(.(..(.((...))...))....)... (.((.(..(.((...))...))....)).) >CP000141.1/1949543-1949572 GUUUCAAUCCCAGAUUGGUUCGAUUAAAAC ...(.(...............)....)... ...(.(..(.(.....)...))....)... ...(.(..(.((...))...))....)... (.((.(..(.((...))...))....)).) >AP009389.1/2004616-2004645 GUUUCAAUUCCUCAUAGGCAGGCUAAAAAC ...(.(...............)....)... ...(.(..(.(.....)...))....)... ...(.(..(.((...))...))....)... (.((.(..(.((...))...))....)).) >CP000679.1/93287-93316 GUUUCAAUCCCCAAAGGGUAGGCUACAAAC ...(.(...............)....)... ...(.(..(.(.....)...))....)... ...(.(..(.((...))...))....)... (.((.(..(.((...))...))....)).) >CP000568.1/717027-716998 GUUUCAAUUCCUCAUAGGUACGAUACAAAC ...(.(...............)....)... ...(.(..(.(.....)...))....)... ...(.(..(.((...))...))....)... (.((.(..(.((...))...))....)).) >AARF01000280.1/1425-1454 GUUUCAAUUCCUUAUAGGUACGUUAGAAAC ...(..(...............)...)... ...(..(.(.(.....)....))...)... ...(..(.(.((...))....))...)... (.((..(.(.((...))....))...)).) >CP000673.1/1722241-1722270 GUUUCAAUUCCUUAUAGGUAGUCUAAAAUC ...(.(...............)...).... ...(..(.(.(.....)...))...).... ...(..(.(.((...))...))...).... (.((..(.(.((...))...))...)).). >AP008230.1/3154402-3154431 GUUUCAAUCCCUCAUAGGUAAGCUAACAAC ...(.(...............)....)... ..(.(..(..(.....)...)).....).. ..(.(..(..((...))...)).....).. >CP000771.1/1024868-1024839 GUUUCAAUCCCUAAUAGGUAUGCUAAAAGC ...(.(...............)....)... ...(.(...(.(....)...))....)... >CP001336.1/4172990-4173019 AUUUCAAUUCCUUAUAGGUAAGCUAACAAC ...(.(...............).....).. ...(..(.(.(.....)...))...).... >CP000612.1/587612-587583 GUUUCAAUUCCUUAUAGGUAGGCUGAUAAC .(...(...............)......). >CP000879.1/2085036-2085007 GUUUCCAUUCCUUAUAGGUAGGAUAAAAAG ...(.(...............)....)...

	ORB			p-value	ORB frequency (per structure per nucleotide)	Means ratio
1	(.Y.().UA.)			< 0.001		31.7

CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC .........1.........2.........3 123456789012345678901234567890
2	(.C.().GNN.)			< 0.001		38.7

CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC .........1.........2.........3 123456789012345678901234567890
3	(.A.)			< 0.001		3.26

CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC .........1.........2.........3 123456789012345678901234567890
4	(U()A)			< 0.001		17.8

CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC .........1.........2.........3 123456789012345678901234567890
	ORB			p-value	ORB frequency (per structure per nucleotide)	Means ratio

	NCM			p-value	NCM frequency (per structure per nucleotide)	Means ratio
1	(.Y.().UA.)			< 0.001		31.7

CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC .........1.........2.........3 123456789012345678901234567890
	NCM			p-value	NCM frequency (per structure per nucleotide)	Means ratio

Structure is visualized using R2R 1.0.6 (Zasha Weinberg).
LOGOS are generated with ggseqlogo (Omar Wagih).