# Analyse et Visualisation de structures 2D d'ARN

Fabrice Leclerc

► To cite this version:

Fabrice Leclerc. Analyse et Visualisation de structures 2D d'ARN. Master. Paris, France. 2020. hal-03313812

HAL Id: hal-03313812

https://hal.science/hal-03313812v1

Submitted on 4 Aug 2021

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<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons CC0 1.0 - Universal - International License
<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

BGA 2020

<figure><img src="image_4.png" /></figure>

# Analyse et Visualisation de structures 2D d'ARN

Fabrice Leclerc, Ph. D., I2BC (Campus d'Orsay)

fabrice.leclerc@universite-paris-saclay.fr
# Echelles de taille et complexité

longueur, repliements (jonctions), interactions à longue distance

<figure><img src="image_5.png" /></figure>

VARNA, S2S, etc

RNAfdl
(intersection-free)
# Motifs ARN

## Représentations 2D

<figure><img src="image_6.png" /><figcaption>ARN simple brin / ARN double brin
fonction / structure</figcaption></figure>
# Jonctions: « 3-way »

## Représentations 2D (3D)

### Une jonction

<figure><img src="image_7.png" /></figure>

### Trois empilements

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>

### Neuf configurations

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>

### Pour chaque configuration, un score

<table><thead><tr><td>Empil.</td><td>Famille</td><td>Score</td></tr></thead><tbody><tr><td>1</td><td>A</td><td>2,12</td></tr><tr><td>1</td><td>B</td><td>0,23</td></tr><tr><td>1</td><td>C</td><td>0,85</td></tr><tr><td>2</td><td>A</td><td>1,5</td></tr><tr><td>2</td><td>B</td><td>0,12</td></tr><tr><td>2</td><td>C</td><td>0,01</td></tr><tr><td>3</td><td>A</td><td>1,3</td></tr><tr><td>3</td><td>B</td><td>0,1</td></tr><tr><td>3</td><td>C</td><td>1,1</td></tr></tbody></table>

Le meilleur score est notre prédiction

<figure><img src="image_19.png" /></figure>
# Jonctions: « 4-way »

## Représentations 2D (3D)

<figure><img src="image_20.png" /><figcaption>Famille $\pi$</figcaption></figure>

<figure><img src="image_21.png" /><figcaption>Famille cH</figcaption></figure>

<figure><img src="image_22.png" /><figcaption>Famille cL</figcaption></figure>

<figure><img src="image_23.png" /><figcaption>Famille cW</figcaption></figure>

<figure><img src="image_24.png" /><figcaption>Famille cK</figcaption></figure>

<figure><img src="image_25.png" /><figcaption>Famille X</figcaption></figure>

<figure><img src="image_26.png" /><figcaption>Famille $\psi$</figcaption></figure>

<figure><img src="image_27.png" /><figcaption>Famille cX</figcaption></figure>

<figure><img src="image_28.png" /></figure>
Structure modulaire

<figure><img src="image_29.png" /></figure>
# Motifs: structure & function

## A. RNA structural motifs

<figure><img src="image_30.png" /><figcaption>Watson-Crick (WC)</figcaption></figure>

<figure><img src="image_31.png" /><figcaption>kissing-loop</figcaption></figure>

<figure><img src="image_32.png" /><figcaption>loop-receptor (LR)</figcaption></figure>

<figure><img src="image_33.png" /><figcaption>three-way junction</figcaption></figure>

<figure><img src="image_34.png" /><figcaption>pseudoknot</figcaption></figure>

## B. RNP interacting motifs

<figure><img src="image_35.png" /><figcaption>ssRNA</figcaption></figure>

<figure><img src="image_36.png" /><figcaption>dsRNA</figcaption></figure>

<figure><img src="image_37.png" /><figcaption>stem-loop</figcaption></figure>

<figure><img src="image_38.png" /><figcaption>internal-loop</figcaption></figure>

<figure><img src="image_39.png" /><figcaption>kink-turn</figcaption></figure>
ARNr 16S

Secondary Structure: small subunit ribosomal RNA

<figure><img src="image_40.png" /></figure>

Escherichia coli

(J01695)

1.cellular organisms 2.Bacteria 3.Proteobacteria

4.gamma subdivision

5. Enterobacteriaceae and related symbionts

6. Enterobacteriaceae 7. Escherichia

November 1999 (cosmetic changes July 2001)

Symbols Used In This Diagram:

G — C — Canonical base pair (A-U, G-C)

G • U — G-U base pair

G • A — G-A base pair

U • U — Non-canonical base pair

Every 10th nucleotide is marked with a tick mark, and every 50th nucleotide is numbered.
<caption>ARNr 16S</caption>

Secondary Structure: small subunit ribosomal RNA

<figure><img src="image_41.png" /></figure>

Escherichia coli

(J01695)

1.cellular organisms 2.Bacteria 3.Proteobacteria

4.gamma subdivision

5. Enterobacteriaceae and related symbionts

6. Enterobacteriaceae 7. Escherichia

November 1999 (cosmetic changes July 2001)

Symbols Used In This Diagram:

G — C - Canonical base pair (A-U, G-C)

G • U - G-U base pair

G O A - G-A base pair

U • U - Non-canonical base pair

Every 10th nucleotide is marked with a tick mark, and every 50th nucleotide is numbered.
<figure><img src="image_42.png" /></figure>

* modèles 2D (expérimental: « footprinting », fluorescence, SHAPE, etc; théoriques: MFold, RNAfold, etc)

* représentations 2D à partir de structures 3D d'ARN

* annotations des structures avec des informations: structurales, functionelles, phylogénétiques, etc
<figure><img src="image_43.png" /><figcaption>VARNA</figcaption></figure>

<figure><img src="image_44.png" /></figure>

<figure><img src="image_45.png" /></figure>

* modèles 2D (expérimental: « footprinting », fluorescence, SHAPE, etc; théoriques: MFold, RNAfold, etc)

<figure><img src="image_46.png" /></figure>

* représentations 2D à partir de structures 3D d'ARN

<figure><img src="image_47.png" /></figure>

* annotations des structures avec des informations: structurales, functionelles, phylogénétiques, etc
<figure><img src="image_48.png" /><figcaption>PseudoViewer</figcaption></figure>

* modèles 2D (expérimental: « footprinting », fluorescence, SHAPE, etc; théoriques: MFold, RNAfold, etc)

* représentations 2D à partir de structures 3D d'ARN

* annotations des structures avec des informations: structurales, functionelles, phylogénétiques, etc
# RNA 2D Structure by HT-SHAPE

<figure><img src="image_49.png" /><figcaption>A. Sample Preparation</figcaption></figure>

electrophilic reagent, e.g. NMIA

$Mg^{2+}$

$^{32}$P labeled primer

fluorescently labeled primers

<figure><img src="image_50.png" /><figcaption>B. RNA Folding and Chemical Modification</figcaption></figure>

<figure><img src="image_51.png" /><figcaption>HIGH-THROUGHPUT SHAPE</figcaption></figure>

<figure><img src="image_52.png" /><figcaption>C. Reverse Transcription</figcaption></figure>

<figure><img src="image_53.png" /><figcaption>D. Fragment Separation</figcaption></figure>

<figure><img src="image_54.png" /><figcaption>F. RNA Structure Prediction</figcaption></figure>

<figure><img src="image_55.png" /></figure>
<figure><img src="image_56.png" /></figure>
# IUPAC nucleotide code

<table><caption>Table 1. IUPAC system for nucleotide nomenclature</caption><thead><tr><td>Single-letter Code</td><td>Nucleotide/s</td><td>Explanation</td></tr></thead><tbody><tr><td>A</td><td>A</td><td>Adenine</td></tr><tr><td>C</td><td>C</td><td>Cytosine</td></tr><tr><td>G</td><td>G</td><td>Guanine</td></tr><tr><td>T / U</td><td>T / U</td><td>Thymine / Uracile</td></tr><tr><td>I</td><td>I</td><td>Inosine</td></tr><tr><td>R</td><td>A or G</td><td>puRine</td></tr><tr><td>Y</td><td>C or T / U</td><td>pYrimidine</td></tr><tr><td>M</td><td>A or C</td><td>aMino</td></tr><tr><td>K</td><td>G or T / U</td><td>Keto</td></tr><tr><td>S</td><td>C or G</td><td>Strong interaction</td></tr><tr><td>W</td><td>A or T / U</td><td>Weak interaction</td></tr><tr><td>H</td><td>A or C or T / U</td><td>not G, H follows G in alphabet</td></tr><tr><td>B</td><td>C or G or T / U</td><td>not A, B follows A in alphabet</td></tr><tr><td>V</td><td>A or C or G</td><td>not T/U, V follows U in alphabet</td></tr><tr><td>D</td><td>A or G or T / U</td><td>not C, D follows C in alphabet</td></tr><tr><td>N</td><td>A or C or G or T/U</td><td>aNy</td></tr></tbody></table>
A Raw Data

<figure><img src="image_57.png" /></figure>

B RNA-Aware Tools

<figure><img src="image_58.png" /></figure>

C Post-Processing

<figure><img src="image_59.png" /></figure>

Rougier, JDEV2013

D Rasterization (Optional)

<figure><img src="image_60.png" /></figure>
# Formats et Outils

<figure><img src="image_61.png" /></figure>
Notation « dot-bracket »

> Rat Alanine tRNA

GAGGAUUUAGCUUAAUUAAAGCAGUUGAUUUGCAUUUAACAGAUGUAAGAUAUAGUCUUACAGUCCUUA

<figure><img src="image_62.png" /><figcaption>Vienna, DBN</figcaption></figure>
Format Stockholm

# STOCKHOLM 1.0

#=GF ID mir-22

#=GF AC RF00653

...

o.latipes.1 CGUUG.CCUCACAGUCGUUCUUCA.CUGGCU.AGCUUUAUGUCCCACG..

Gasterosteus_aculeat.1 GGCUG.ACCUACAGCAGUUCUUCA.CUGGCA.AGCUUUAUGUCCUCAUCU

R.esox.1 AGCUGAGCACA...CAGUUCUUCA.CUGGCA.GCCUUAAGGUUUCUGUAG

...

#=GC SS_cons .<<<<<<.<<.<<<<<<<<<.<<<<<<.<<<<<<<<<.■<........

#=GC RF gGccg.acucaCagcaGuuCuuCa.cuGGCA.aGCuuuAuguccuuauaa

O.latipes.1 CCCCACCGUAAAGCU.GC.CAGUUGAAGAGCUGUUGUG..UGUAACC

Gasterosteus_aculeat.1 ACCAGC..UAAAGCU.GC.CAGCUGAAGAACUGUUGUG..GUCGGCA

R.esox.1 ACAGGC..UAAACCU.GC.CAGCUGAAGAACUGCUCUG..GCCAGCU

...

#=GC SS_cons ...>>.>>><>>.>>.>>.>>><>>><>>><>>>.>>><>>.

#=GC RF acaaac..UaaaGCu.GC.CaGuuGaaGaaCugcuGug..gucggCu

//
# Stockholm - Ralee (emacs)

\# STOCKHOLM 1.0

Pho21_215834-215776 -

Pfu21_163991-163933 -

Pab21_230575-230517 -

Consensus

\# =GC SS_cons

//

CGGCCCCGTTCCCGCCCTCTCCGGGGAATCGTGAACCGGGGGTTCCGACCGGGCCGACA

GGGCCCCGTTCCCGCCCTCTCCGGGGAATCGTGAACCGGGGGTTCCGACCGGGCCCA

GGGCCCCGGCTCCCGCCCTCTCCGGGGAATCGTGAACCGGGGGTTCCGGCCGGGCCTACA

GGGCCCCGUUCCCGCCCUCUCCGGGAAUCGUGAACCGGGGGUUCCGACCGGGCCCA

<<<<<<<<<...<<<...<<<........>>>>>>>>...>>>>>>

\# STOCKHOLM 1.0

Pab105_1335797-1335648 -

Pho105_592081-592230 +

Pfu105_942696-942544 -

Consensus

\# =GC SS_cons

//

CCGCCCCGA-GGCCCCGACCGAGGGAGCGTGCCGAGAAAGGCGCGCCATGAACGAGGCGACGTCGCCGGGCGGACAGGGCCCGGTCTCCGGGG

CCGCCCCGGG-GGCCCCGACCGAGGGAGCGTGCCGAGAATGGCGCGCAATGAACGAGGTGACGTCGTCGGGCGGACAGGGCCCGGTCTCCGGGG

CCGCCCCGGGCGGCCCGACCGAGGGAGCGTGCCGGCAATGGCGCGCGATGAACGAGGTGACGTCTCCGGGCGGACAGGGCCCGGCCTTCGGGG

CCGCCCCGG-GGCCCCGACCGAGGGAGCGUGCCGAGAAUGGCGCGCAAUGAACGAGGUGACGUCGCCGGGCGGACAGGGCCCGGUCUCCGGGG

<<<<<<<<<...<<<<...>>>...<<<<<<...>>>>>>>>...<<...<<...>>>...>>>>>>>>...<<<<<<<<<...<<<<...

Pab105_1335797-1335648 -

Pfu105_942696-942544 -

Consensus

\# =GC SS_cons

//

CCGCCTGAGGTTGCCGACAACGGCGGGCAATGAGGGCGGGTGGATAAGCCGGGCCTATA--

CCGCCTGAGGTTGCCGAGAATGGCGTTCAATGAAGGCGGGCGGATAATCCGGGCCTAAA--

CCGCCTGAGGGAGCCGAGAAGGGCAGACGATGAAGGCGGGCGGATAAGCCGGGCCCTCAAA

CCGCCUGAGGUUGCCGAGAACGGCGGACAAUGAAGGCGGGCGGAUAAGCCGGGCCUAAA--

<<<<<<<...<<<...>>>>...........>>>>...>>>>>>...>>>>>>>>...
# Stockholm - Rfam

# STOCKHOLM 1.0
#=GF ID snoR9
#=GF AC RF00065
#=GF DE Small nucleolar RNA snoR9
#=GF AU Bateman A, Daub J
#=GF GA 50.0
#=GF NC 49.8
#=GF TC 68.7
#=GF SE Bateman A
#=GF SS Published; PMID:12032319
#=GF TP Gene; snRNA; snoRNA; CD-box;
#=GF BM cmbuild -F CM SEED; cmcalibrate --mpi -s 1 CM
#=GF BM cmsearch -Z 274931 -E 1000000 --toponly CM SEQDB
#=GF DR SO:0000593 SO:C_D_box_snoRNA
#=GF DR GO:0006396 GO:RNA processing
#=GF DR GO:0005730 GO:nucleolus
#=GF RN [1]
#=GF RM 12032319
#=GF RT Noncoding RNA genes identified in AT-rich hyperthermophiles.
#=GF RA Klein RJ, Misulovin Z, Eddy SR;
#=GF RL Proc Natl Acad Sci U S A 2002;99:7542-7547.
#=GF CC snoRNA R9 is a member of the C/D class of snoRNA which contain
#=GF CC the C (UGAUGA) and D (CUGA) box motifs. R9 was identified in a
#=GF CC computational screen in AT-rich hyperthermophiles [1]. R9 was
#=GF CC found to overlap with the smaller snoRNA R19 which is currently a
#=GF CC member of Pyrococcus C/D box snoRNA family Rfam:RF00095.
#=GF WK http://en.wikipedia.org/wiki/Small_nucleolar_RNA_snoR9
#=GF SQ 5

#=GS Pyrococcus_furiosus AC AE009950.1/163991-163864
#=GS Pyrococcus_abyssi_GE AC AJ248283.1/230575-230449
#=GS Pyrococcus_horikoshi AC BA000001.2/215834-215709
#=GS P.furiosus AC AF468960.1/1-128
#=GS Thermococcus_kodakar AC AP006878.1/47908-47779
Stockholm - Rfam

#=GS Pyrococcus_furiosus AC AE009950.1/163991-163864
#=GS Pyrococcus_abyssi_GE AC AJ248283.1/230575-230449
#=GS Pyrococcus_horikoshi AC BA000001.2/215834-215709
#=GS P.furiosus AC AF468960.1/1-128
#=GS Thermococcus_kodakar AC AP006878.1/47908-47779

Pyrococcus_furiosus
Pyrococcus_abyssi_GE
Pyrococcus_horikoshi
P.furiosus
Thermococcus_kodakar
#=GC SS_cons
#=GC RF

Pyrococcus_furiosus
Pyrococcus_abyssi_GE
Pyrococcus_horikoshi
P.furiosus
Thermococcus_kodakar
#=GC SS_cons
#=GC RF

Pyrococcus_furiosus
Pyrococcus_abyssi_GE
Pyrococcus_horikoshi
P.furiosus
Thermococcus_kodakar
#=GC SS_cons
#=GC RF

//

GGGCCCCGUU.CCCGCCCUCUCCGGGAAUCGUGAACCGGGGGUUCCGAC
GGGCCCCGCU.CCCGCCCUCUCCGGGAAUCGUGAACCGGGGGUUCCGGC
CGGCCCCGUU.CCCGCCCUCUCCGGGAAUCGUGAACCGGGGGUUCCGAC
GGGCCCCGUU.CCCGCCCUCUCCGGGAAUCGUGAACCGGGGGUUCCGAC
GGGCCUGGCUCCCGCCCUCUCCCGGGAAACGUGAACCGGGGCUUCCUGC
<<<<<<<<<........<<<<<<<<<<.....>>>>>>></<<<<<<
gGGCCCGGcu.CCCgCCCUCUCCGGGAAUCGUGAACCGGGGGuUCCggC

CGGGCCCACA..AUGGGAUGAUGACCUUUUGCUUUACUGAACACAUGAUG
CGGGCCUACA..G..UUAUGAUGAACUUUUGCUUUUGCUGAUGUGGUGAUG
CGGGCCGACA..GG.GGAUGAAGAGCUUUUGCUUUUGCUGAGCAGAUGAUG
CGGGCCCACA..AUGGGAUGAUGACCUUUUGCUUUACUGAACACAUGAUG
CAGGCCUACACCGGGGGAUGAAGAGCUUUUGCUUUUGCUGAC..UGUGAUG
>>>>>>><....................................................
CGGGCCcACA..auguuAUGAUGAaCUUUUGCUUUaCUGAagagaUGAUG

ACCACGCCCUUCGCUGAC.CUAAAUAUUUGAC
AGCACGCCCUUCGCUGAUACUCUCUCGUCCAU
ACCACGCCCUUCGCUGAC.CU.GCUAUUUUGAC
ACCACGCCCUUCGCUGAC.CUAAAUAUUUGAC
AGCACGCCCUUCACUGACCCCGUAUCAGCUCU
....................................................
AgCACGCCCUUCGCUGAu.CUaaaUauUugAu
Stockholm - R2R

<figure><img src="image_63.png" /><figcaption>## RF00065_seed Pyrococcus_abyssi_GERF00065_seed Pyrococcus_furiosus</figcaption></figure>

<figure><img src="image_64.png" /></figure>

Stockholm
Stockholm - R2R

<figure><img src="image_65.png" /><figcaption>RF00065_seed skeleton-with-bp</figcaption></figure>

<figure><img src="image_66.png" /><figcaption>RF00065_seed-ILOOP75</figcaption></figure>

subfam_weight=0.696064

<figure><img src="image_67.png" /><figcaption>RF00065_seed-ILOOP85</figcaption></figure>

subfam_weight=0.303936

<figure><img src="image_68.png" /></figure>

Stockholm
# Pseudo-nœuds (pseudoknots)

<figure><img src="image_69.png" /></figure>

* Définition: structure 2D d'acide nucléique contenant au moins 2 tige-boucle dans laquelle la moitié de l'une est intercalée entre les 2 autres moitiés de l'autre

<figure><img src="image_70.png" /></figure>

<figure><img src="image_71.png" /></figure>
# Pseudobase-Pseudoviewer

1590 1600 1610 1620 1630
# |123456789|123456789|123456789|123456789|123456
$ 1590 AAAAAACUAAUAGAGGGGGGACUUAGCGCCCCCAAACCGUAACCCC=1636
% 1590 :: :: :: :: :: :: :: :: :: :: ::

<figure><img src="image_72.png" /></figure>

PseudoViewer

Pseudobase
# Représentations circulaires

<figure><img src="image_73.png" /></figure>

VARNA

<figure><img src="image_74.png" /></figure>

Vienna / DBN; Connect

jViz.RNA
# Ribozyme HDV (RF00059)

<figure><img src="image_75.png" /></figure>

VARNA

RF00059_seed

<figure><img src="image_76.png" /></figure>

Vienna / DBN; Stockholm

R2R
ARNr 16S (T. thermophilus)

<figure><img src="image_77.png" /></figure>

Thermus thermophilus

(X07998)

1. cellular organisms 2. Bacteria

3. Thermus/Deinococcus group

4. Thermus group 5. Thermus

September 2001
# Structures 2D alternatives

<figure><img src="image_78.png" /><figcaption>RIBOSWITCH</figcaption></figure>

<figure><img src="image_79.png" /><figcaption>VARNA</figcaption></figure>

<caption>Vienna/DBN</caption>

<caption>conformation 2 (OFF)</caption>
# Probabilité de structures 2D

mutations, données d'accessibilité

with chemical mapping data

<figure><img src="image_80.png" /></figure>

GGaCUCGGCUUGCUGaaGCGCGCACGGCAAAGAGGCGAGGGgCGGCgACUGGUGAGuACGCcaaaaAUUUUGACUAGCGgAGGCUAgaAGgAgAgAC

GGACUCGGCUUGCUGAAGCGCGCACGGCAAAGAGGCGAGGGGCGGCGACUGGUGAGUACGCCAAAAAUUUUGACUAGCGGAGGCUAGAAGGAGAGAC

base pairing 1

<figure><img src="image_81.png" /></figure>

base pairing 2

<figure><img src="image_82.png" /></figure>

HIV 5' UTR

**RNAbows**

Aalberts & Jannen, RNA, 2013
# Pseudo-nœuds

A

<figure><img src="image_83.png" /></figure>

B

<figure><img src="image_84.png" /></figure>

C

<figure><img src="image_85.png" /></figure>

jViz.RNA

PseudoViewer

D

<figure><img src="image_86.png" /></figure>

VARNA
# Appariements & nomenclature

<table><thead><tr><th rowspan="2">No.</th><th rowspan="2">Glycosidic bond orientation</th><th colspan="2">Interacting edges</th><th rowspan="2">Abbreviation</th><th rowspan="2">Symbol</th><th rowspan="2">Triangle abstraction</th></tr><tr><th>NT1</th><th>NT2</th></tr></thead><tbody><tr><td>1</td><td>Cis</td><td>Watson-crick</td><td>Watson-crick</td><td>cWW</td><td>●</td><td>●●●</td></tr><tr><td>2</td><td>Trans</td><td>Watson-crick</td><td>Watson-crick</td><td>tWW</td><td>○</td><td>○○○</td></tr><tr><td rowspan="2">3</td><td rowspan="2">Cis</td><td>Watson-crick</td><td>Hoogsteen</td><td>cWH</td><td>●●●</td><td>●●●</td></tr><tr><td>Hoogsteen</td><td>Watson-crick</td><td>cHW</td><td>●●●</td><td>●●●</td></tr><tr><td rowspan="2">4</td><td rowspan="2">Trans</td><td>Watson-crick</td><td>Hoogsteen</td><td>tWH</td><td>○○</td><td>○○</td></tr><tr><td>Hoogsteen</td><td>Watson-crick</td><td>tHW</td><td>○○</td><td>○○</td></tr><tr><td rowspan="2">5</td><td rowspan="2">Cis</td><td>Watson-crick</td><td>Sugar edge</td><td>cWS</td><td>●●</td><td>●●</td></tr><tr><td>Sugar edge</td><td>Watson-crick</td><td>cSW</td><td>●●</td><td>●●</td></tr><tr><td rowspan="2">6</td><td rowspan="2">Trans</td><td>Watson-crick</td><td>Sugar edge</td><td>tWS</td><td>○○</td><td>○○</td></tr><tr><td>Sugar edge</td><td>Watson-crick</td><td>tSW</td><td>○○</td><td>○○</td></tr><tr><td>7</td><td>Cis</td><td>Hoogsteen</td><td>Hoogsteen</td><td>cHH</td><td>●</td><td>●●●</td></tr><tr><td>8</td><td>Trans</td><td>Hoogsteen</td><td>Hoogsteen</td><td>tHH</td><td>○</td><td>○○○</td></tr><tr><td rowspan="2">9</td><td rowspan="2">Cis</td><td>Hoogsteen</td><td>Sugar edge</td><td>cHS</td><td>●●</td><td>●●</td></tr><tr><td>Sugar edge</td><td>Hoogsteen</td><td>cSH</td><td>●●</td><td>●●</td></tr><tr><td rowspan="2">10</td><td rowspan="2">Trans</td><td>Hoogsteen</td><td>Sugar edge</td><td>tHS</td><td>○○</td><td>○○</td></tr><tr><td>Sugar edge</td><td>Hoogsteen</td><td>tSH</td><td>○○</td><td>○○</td></tr><tr><td rowspan="2">11</td><td rowspan="2">Cis</td><td>Sugar edge (priority)</td><td>Sugar edge</td><td>cSs</td><td>●●</td><td>●●</td></tr><tr><td>Sugar edge</td><td>Sugar edge (priority)</td><td>csS</td><td>●●</td><td>●●</td></tr><tr><td rowspan="2">12</td><td rowspan="2">Trans</td><td>Sugar edge (priority)</td><td>Sugar edge</td><td>tSs</td><td>○○</td><td>○○</td></tr><tr><td>Sugar edge</td><td>Sugar edge (priority)</td><td>tsS</td><td>○○</td><td>○○</td></tr></tbody></table>

Lentos & Westhof, Curr. Opi. Struct. Biol., 2003

<figure><img src="image_87.png" /></figure>

Stombaugh et al., NAR, 2009
# Motifs ARN & fonction(s)

<figure><img src="image_88.png" /></figure>

flexibilité

<figure><img src="image_89.png" /></figure>

nucléotide(s) non appariés, appariements non canoniques

<figure><img src="image_90.png" /></figure>

structures et “formes” 3D

<figure><img src="image_91.png" /></figure>

appariemments canoniques/non-canoniques & sillons

<figure><img src="image_92.png" /></figure>

interactions: ARN-ARN, ARN-protéine, ARN-ligand, ...

<figure><img src="image_93.png" /></figure>

régions simple/double-brin, formes et contacts
Bulges: flexibilité & interaction

<figure><img src="image_94.png" /><figcaption>(b)</figcaption></figure>

<figure><img src="image_95.png" /><figcaption>(c)</figcaption></figure>

<figure><img src="image_96.png" /><figcaption>(d)</figcaption></figure>

<figure><img src="image_97.png" /></figure>

Structure
# Appariements & sillons

## appariements non-canoniques et ouverture du grand sillon

<figure><img src="image_98.png" /></figure>

<figure><img src="image_99.png" /></figure>

## ARN de liaison à la protéine Rev (VIH-1)

Leclerc *et al.*, Nat. Struct. Biol., 1994; Leclerc *et al.*, Fold. Des., 1997
# Motifs récurrents

## Known motifs

<figure><img src="image_100.png" /><figcaption>(C)
C-loop</figcaption></figure>

<figure><img src="image_101.png" /><figcaption>(K)
K-turn</figcaption></figure>

<figure><img src="image_102.png" /><figcaption>(S)
Sarcin-ricin</figcaption></figure>

<figure><img src="image_103.png" /><figcaption>(H)
Hook-turn</figcaption></figure>

<figure><img src="image_104.png" /><figcaption>(A)
A-minor</figcaption></figure>

<figure><img src="image_105.png" /><figcaption>(E)
E-loop</figcaption></figure>

<figure><img src="image_106.png" /><figcaption>(F)
E-loop</figcaption></figure>

<figure><img src="image_107.png" /><figcaption>(G)
E-loop</figcaption></figure>

<figure><img src="image_108.png" /><figcaption>(R)
Reverse-Kturn</figcaption></figure>

<figure><img src="image_109.png" /><figcaption>(T)
Tandem sheared</figcaption></figure>
# Motifs ARN 3D & “formes”

A

<figure><img src="image_110.png" /></figure>

1A4D: Loop D/Loop E arm

B

<figure><img src="image_111.png" /></figure>

1CSL: HIV RRE high affinity site

C

<figure><img src="image_112.png" /></figure>

1I9X: branchpoint duplex from U2 snRNA

D

<figure><img src="image_113.png" /></figure>

1KKA: unmodified anticodon Phe stem-loop

E

<figure><img src="image_114.png" /></figure>

2A43: luteovirus pseudoknot

F

<figure><img src="image_115.png" /></figure>

1GID: over-twisted P5b helix from *Tetrahymena* ribozyme

G

<figure><img src="image_116.png" /></figure>

354D: loop E motif from *E. coli* 5S rRNA

H

<figure><img src="image_117.png" /></figure>

2GIS: kink-turn motif from SAM-I riboswitch

I

<figure><img src="image_118.png" /></figure>

4P8Z: A-minor contact from group I intron

J

<figure><img src="image_119.png" /></figure>

2R8S: tetraloop/receptor from *Tetrahymena* ribozyme
Motif Kink-turn (K-loop)

<figure><img src="image_120.png" /></figure>
<figure><img src="image_121.png" /><figcaption>ARNr 16S</figcaption></figure>

Escherichia coli

(J01695)

1.cellular organisms 2.Bacteria 3.Proteobacteria

4.gamma subdivision

5. Enterobacteriaceae and related symbionts

6. Enterobacteriaceae 7. Escherichia

November 1999 (cosmetic changes July 2001)

Symbols Used In This Diagram:

G — C - Canonical base pair (A-U, G-C)

G • U - G-U base pair

G ○ A - G-A base pair

U • U - Non-canonical base pair

Every 10th nucleotide is marked with a tick mark, and every 50th nucleotide is numbered.
Motifs 2D K-turn

<figure><img src="image_122.png" /></figure>
Motifs K-turn & interactions

<figure><img src="image_123.png" /></figure>
# Données phylogénétiques

<figure><img src="image_124.png" /></figure>

<footnote>* post-processing</footnote>
# Le ribozyme à tête de marteau

## HHR

### Type II Hammerhead Consensus

<figure><img src="image_125.png" /></figure>

- covarying mutations

- compatible mutations

R = purine; Y = pyrimidine

<figure><img src="image_126.png" /></figure>

variable-length hairpin

<figure><img src="image_127.png" /><figcaption>marine metagenome</figcaption></figure>

<figure><img src="image_128.png" /><figcaption>Drosophila pseudoobscura</figcaption></figure>

<figure><img src="image_129.png" /><figcaption>Yarrowia lipolytica</figcaption></figure>

<figure><img src="image_130.png" /><figcaption>mouse gut metagenome</figcaption></figure>
Diagrammes Arc

covariations, conservation

R-Chie

<figure><img src="image_131.png" /></figure>

RFAM: RF00065

Stockholm
# Structures 2D conservées

<figure><img src="image_132.png" /><figcaption>## Pab-40</figcaption></figure>

# STOCKHOLM 1.0

Ph40.2-2673-2678 GCCCGGCCc.ttagcgaggtc...CCCTcgG..GAggcgccttccgcgtcacggagtgccGTGA.ccGGGGG...taaccct.gGCCGGGC..ACA

Pa40.2-2678 GCCCGGCCc.tcagcgaggtc...CCCTcgG..TAggtgccttccgcgtcacggagccGTGA.ccGGGGG...taaccct.gGCCGGGC..ACA

Pf7.2-2701-2678 GCCCGGCCc.tcagcgaggtc...CCCTcgG..GAggtgccttccgcgtcacggagtgccGTGA.ccGGGGG...taaccct.gGCCGGGC..ACA

# STOCKHOLM 1.0

Pa40.2-1932 GCCCGGCCcucagcgagguCCCCUcgGUAggugccuuccgcgucacgGAgcgccGUGAccGGGGGuaaccug GCCGGGCACA

Ph40.2-2673-78 GCCCGGCCcuuagcgagguCCCCUcgGGAggcccuuccgcgucacggagugccGUGAccGGGGGuaaccug GCCGGGCACA

Pf7.2-2701-2678 GCCCGGCCcucagcgagguCCCCUcgGGAggugccuuccgcgucacggagugccGUGAccGGGGGuaaccug GCCGGGCACA

#=GC SS_cons <<<<<<<<<...<<<<<<...>>>>> ...<<<...<<<...>>>>> ...

//

Stockholm
# Alignements

## CLUSTALW

<table><tr><td>interORF_Pyro_furi_347</td><td>GCAATAAGGAGT AGGCTCAGGAAGCCGTCCACTCCTCACCAATCAGGTGCGGAAGGCATCATCATCGCCTTACCTCCC</td><td>79</td></tr><tr><td>interORF_Pyro_hori_397</td><td>GCAATAAGGAGT-AGGCTCAGGAAGCCGTCCACTCCTCATTCAGGTGCGGAAGGCTTCATCATCGCCTTCTTTACT</td><td>79</td></tr><tr><td>interORF_Pyro_abys_654</td><td>GCGTATAAGGAGTGAGGCTCAGGAAGCCGTCCACTCCTCACCGTTCAGGTGCGGAAGGCTTCATCATTGCCATTTATATT</td><td>80</td></tr><tr><td>ruler</td><td>1......10......20......30......40......50......60......70......80</td><td></td></tr></table>

<figure><img src="image_133.png" /></figure>

<table><tr><td>**</td><td>*</td><td>***</td><td>***</td><td>***</td><td>*</td><td>*</td><td>*</td><td>*</td><td>***</td><td>*</td><td>*</td></tr><tr><td>interORF_Pyro_furi_347</td><td>TTAGATTCCCTATGTTTTAATCTAATCTTGTATCTTTTTAACATTCTTACGTCAAATA</td><td>138</td></tr><tr><td>interORF_Pyro_hori_397</td><td>TTAT-TGTTAAAAGTTTATAAGGTAAACTAATAGCATTTAAACAGCTAGAATTTGTAAA</td><td>137</td></tr><tr><td>interORF_Pyro_abys_654</td><td>TTCTTCATGTAAGTTTTATAAATTAACCCGATTATTTCTAACGATGATAGTAGGCCTA</td><td>139</td></tr><tr><td>ruler</td><td>90......100......110......120......130......</td><td></td></tr></table>

<figure><img src="image_134.png" /></figure>

# STOCKHOLM 1.0

interORF_Pyro_abys_654
interORF_Pyro_furi_347
interORF_Pyro_hori_397
Consensus
#=GC SS_cons

interORF_Pyro_abys_654
interORF_Pyro_furi_347
interORF_Pyro_hori_397
Consensus
#=GC SS_cons
//

GCGTATAAGGAGTGAGGCTCAGGAAGCCGTCCACTCCTCACCGTTCAGGTGCGGAAGGCTTCATCATTGCCATTTATATT
GCATAAAGGAGT-AGGCTCAGGAAGCCGTCCACTCCTCACCAATCAGGTGCGGAAGGCATCATCATCGCCTTACCTCCC
GCATAAAGGAGT-AGGCTCAGGAAGCCGTCCACTCCTCATTCAGGTGCGGAAGGCTTCATCATCGCCTTCTTTACT
GCAUAUAAGGAGU_AGGCUCAGGAAGCCGUCCACUCCUCACCAUUCAGGUGCGGAAGGCUUCAUCAUCGCCUUAAUACU
<<<......<<<...<<<......>>>>......>>>>>><<<......>>>>>><<<<<<<......>>>>>>......

TTCTTCATGTAAGTTTTATAAATTAACCCGATTATTTCTCAACGATGATA---GTAGGCCTAA
TTAGATTCCCTTATGTTTTAATCTAATCTTGTATCTTTTTAACATTCTTA---CGTCAAATAAT
TTATTGTTAAAAGTTT-ATAAGGTAAACTAATAGCATTTAAACAGCTAGAATTTGTAAACTTAA
UUAUUCUUUAAGUUUUUAUAAACUAAACUAAUAACUUUUAAACAAUCAUA____GUAACUUAA

Stockholm
Diagrammes Arc

covariations, conservation

R-Chie

<figure><img src="image_135.png" /></figure>

RFAM: RF00065

Stockholm
# ARN à boîtes C/D

## RNAz, RNAalifold

interORF Pyro hori 397
interORF Pyro abys 654
interORF Pyro furi 347
ruler

## Pab C/D sRNA sR1

5' C box D'box C'box D box 3'
......(((........(((((..................)).))))).))))....)).
AAAGAA GGC GAUGA GAAGCC UCCGC ACC GAAUGAUG AGGAG UGGAC GGCUUC CUGAGCC U 63
AUAUAUGGCAAUGAUGAAGCC UCCGC ACC GAACGGUG AGGAG UGGAC GGCUUC CUGAGCC U 63
AGGUAAGGC GAUGAUGAUGCC UCCGC ACC GAUUGGUG AGGAG UGGAC GGCUUC CUGAGCC U 63
......10.........20.........30.........40.........50.........60...

<figure><img src="image_136.png" /></figure>

<figure><img src="image_137.png" /></figure>

Energy = -24.6 kcal/mol

Clustal; Vienna / DBN
# ARN à boîtes H/ACA

## RNAz, RNAalifold

Pho21_215834-215776 -
Pfu21_163991-163933 -
Pab21_230575-230517 -

## Pab-21 H/ACA sRNA

(((((((((...(((...(((...........)))))))))))))
CGGCCCCGGUUUCCC
GGGCCCCGGUUUCCC
GGGCCCCGGCUUCCC
((((((((...(((...(((...........)))))))))))))
GGGCCCCGGUUUCCC
GGGCCCCGGCUUCCC
GGGCCCCGGCUUCCC
((((((((...(((...(((...........)))))))))))))
GGGCCCCGGUUUCCC
GGGCCCCGGCUUCCC
GGGCCCCGGCUUCCC

<figure><img src="image_138.png" /></figure>

Clustal; Vienna/DBN
# ARN à boîtes (H/ACA)n

SSU 891

<figure><img src="image_139.png" /></figure>

Pab-21
1 motif

<figure><img src="image_140.png" /></figure>

Pab-105
2 motifs

<figure><img src="image_141.png" /></figure>

Pab-40
3 motifs
# ARN à boîtes (H/ACA)²

## Pab-105 H/ACA sRNA

<figure><img src="image_142.png" /></figure>

<figure><img src="image_143.png" /></figure>

<figure><img src="image_144.png" /></figure>

Energy = -75.8 kcal/mol

Clustal; Vienna / DBN
# ARN à boîtes (H/ACA)³

## Pab-40 H/ACA sRNA

Pab40_382389-382599 +
Pho40_1597422-1597634 +
Pfu40_1732713-1732926 +
ruler

<figure><img src="image_145.png" /></figure>

Pab40_382389-382599 +
Pho40_1597422-1597634 +
Pfu40_1732713-1732926 +
ruler

<figure><img src="image_146.png" /></figure>

<figure><img src="image_147.png" /></figure>

Clustal; Vienna / DBN
Comparaison 2D

arbre de proximités
entre structures 2D

<figure><img src="image_148.png" /></figure>
Graphes

<figure><img src="image_149.png" /><figcaption>VARNA</figcaption></figure>

<caption>Graphiz
(RNAView)</caption>

((((((...((((...))))((((...))))))...((((...)))))))))...
Empreintes

<figure><img src="image_150.png" /></figure>

VARNA

chimiques, enzymatiques

<figure><img src="image_151.png" /></figure>

Vienna/DBN
# Données fonctionnelles¹

<figure><img src="image_152.png" /><figcaption>## functional annotation</figcaption></figure>

<figure><img src="image_153.png" /></figure>

## VARNA

RFAM: RF00065
# Données fonctionnelles²

<figure><img src="image_154.png" /><figcaption>## functional annotation</figcaption></figure>

<figure><img src="image_155.png" /><figcaption>## VARNA</figcaption></figure>

RFAM: RF00065
# Données fonctionnelles³

<figure><img src="image_156.png" /><figcaption>## H/ACA guide RNA (Archaea)</figcaption></figure>

functional annotation

<figure><img src="image_157.png" /></figure>

5' guide sequence

3' guide sequence

VARNA

RFAM: RF00065
Modifications d'accessibilité

<figure><img src="image_158.png" /><figcaption>VARNA</figcaption></figure>

<figure><img src="image_159.png" /></figure>

<figure><img src="image_160.png" /></figure>

<figure><img src="image_161.png" /><figcaption>Vienna/DBN</figcaption></figure>
# Données d'empreintes¹

<figure><img src="image_162.png" /></figure>

accessibility
annotation

VARNA

RFAM: RF00065

RNA
accessibility

<figure><img src="image_163.png" /></figure>
# Données d'empreintes²

accessibility
annotation

<figure><img src="image_164.png" /></figure>

VARNA

RFAM: RF00065

more
accessible

<figure><img src="image_165.png" /></figure>
# Données d'empreintes³

<figure><img src="image_166.png" /></figure>

accessibility
annotation

VARNA

RFAM: RF00065

<figure><img src="image_167.png" /></figure>

less
accessible
# Données d'empreintes⁴

<figure><img src="image_168.png" /></figure>

accessibility
annotation

VARNA

RFAM: RF00065

<figure><img src="image_169.png" /></figure>
Interactions ARN-ARN

<caption>A</caption>

RILogo

<figure><img src="image_170.png" /><figcaption>C</figcaption></figure>

VARNA

<figure><img src="image_171.png" /></figure>

guide RNA
RFAM: RF00065

Vienna/DBN

<figure><img src="image_172.png" /><figcaption>B</figcaption></figure>

* post-processing

Stockholm
# Gènes H/ACA

A

Pab21

<figure><img src="image_173.png" /></figure>

B

Pab35

<figure><img src="image_174.png" /></figure>

E

Pab105

<figure><img src="image_175.png" /></figure>

G

Pab19

<figure><img src="image_176.png" /></figure>

C

Pab40

<figure><img src="image_177.png" /></figure>

D

Pab91

<figure><img src="image_178.png" /></figure>

F

Pab160

<figure><img src="image_179.png" /></figure>

Pyrococcus

<figure><img src="image_180.png" /></figure>

Thermococcus

7 H/ACA genes

11 H/ACA motifs

Muller *et al.*, NAR, 2008
# Fonction des H/ACA

<figure><img src="image_181.png" /></figure>
# Gènes H/ACA

<figure><img src="image_182.png" /><figcaption>Pyrococcus
&
Thermococcus

7 H/ACA genes
11 H/ACA motifs</figcaption></figure>

Muller *et al.*, NAR, 2008
Repliements H/ACA

<figure><img src="image_183.png" /></figure>

b) p = 0.618

<figure><img src="image_184.png" /></figure>

a) p = 0.382
# H/ACA et leur(s) cible(s)

<figure><img src="image_185.png" /></figure>
# H/ACA: Structure-Fonction

<figure><img src="image_186.png" /></figure>

Pa21-S891*

<figure><img src="image_187.png" /></figure>

10

5

9

<figure><img src="image_188.png" /></figure>

Pa21-S892

<figure><img src="image_189.png" /></figure>

9

6

9

R2R*
# H/ACA « productifs »

<figure><img src="image_190.png" /><figcaption>## Pa21-S891, Ph21-S879, Pf1-S879</figcaption></figure>

<figure><img src="image_191.png" /></figure>

$E = -28.2 \text{ kcal/mol}$

<figure><img src="image_192.png" /><figcaption>## Pa21-S891</figcaption></figure>
# H/ACA « non-productifs »

Pa21-S892, Ph21-S880, Pf1-S880

<figure><img src="image_193.png" /></figure>

<figure><img src="image_194.png" /></figure>

$E = -24.5$ kcal/mol

Pa21-S892

<figure><img src="image_195.png" /></figure>
# Familles H/ACA

<figure><img src="image_196.png" /><figcaption>## Pa_HACA-GUIDE65</figcaption></figure>

<figure><img src="image_197.png" /></figure>

subfam_weight=0.284006

<figure><img src="image_198.png" /><figcaption>## Pa_HACA-GUIDE66</figcaption></figure>

subfam_weight=0.163641

<figure><img src="image_199.png" /><figcaption>## Pa_HACA-GUIDE55</figcaption></figure>

subfam_weight=0.120714

<figure><img src="image_200.png" /><figcaption>## Pa_HACA-GUIDE56</figcaption></figure>

subfam_weight=0.215373

<figure><img src="image_201.png" /><figcaption>## Pa_HACA-GUIDE75</figcaption></figure>

subfam_weight=0.106001

<figure><img src="image_202.png" /><figcaption>## Pa_HACA-GUIDE85</figcaption></figure>

subfam_weight=0.110265

base pair annotations
covarying mutations
compatible mutations
no mutations observed

<figure><img src="image_203.png" /></figure>
# Interactions intra-moléculaires

<figure><img src="image_204.png" /></figure>

VARNA

<figure><img src="image_205.png" /></figure>
# Interactions inter-moléculaires

<figure><img src="image_206.png" /></figure>

IntaRNA

Leclerc *et al.*, Sci. Rep., 2016

VARNA
# Interactions inter-moléculaires

<figure><img src="image_207.png" /></figure>

monomer 1

<figure><img src="image_208.png" /></figure>

monomer 2

<figure><img src="image_209.png" /></figure>
# Interactions inter-moléculaires

<figure><img src="image_210.png" /></figure>

monomer 1 HI

IntaRNA

monomer 1

monomer 2

Leclerc *et al.*, Sci. Rep., 2016

monomer 2

VARNA
Conclusions

❖ représentations standardisées et personnalisées (édition, annotation)

❖ gain de temps pour la génération de représentations multiples

❖ gain de temps pour la mise à jour de structures consensus

❖ outils qualitatif (quantitatif) pour évaluer des modèles structure-function
Outils & Ressources

* RFAM (**VARNA**), Comparative RNA Web Site & Project (RNA2DMap, CT, BPSEQ), The RNA Mapping Database - RMDB (**RDAT**, **RNAstructure**), ...

* packages: Vienna Package (**RNAfold**, **RNAalifold**, etc), Boulder Alignment Editor (**VARNA**), SAVor (**RNAfold**, **RNAplot**), S2S/Assemble 2D & 3D, Jalview 2D & 3D (**VARNA**, **Jmol**), ...

* outils récents: long RNAs: **RNAfdl**, pairing probabilities (alternative conformations): **RNAbow**, **RNAllViewer**, ...
Références

❖ Ponty Y. & Leclerc F., Drawing and editing the Secondary Structures of RNA(s), Methods in Molecular Biology, 2015.

❖ Aigner K. et al., Chapitre 9. Visualizing RNA sequence and structure, 2011.
Acknowledgments

<figure><img src="image_211.png" /></figure>

université
PARIS-SACLAY

<figure><img src="image_212.png" /></figure>

<figure><img src="image_213.png" /></figure>

<figure><img src="image_214.png" /></figure>

<figure><img src="image_215.png" /></figure>
De la séquence au 2D

<figure><img src="image_216.png" /></figure>
# De la structure 2D à 3D

<figure><img src="image_217.png" /></figure>

* la structure 2D: une contrainte géométrique "forte"

<figure><img src="image_218.png" /></figure>

* appariements non-canoniques et motifs

<figure><img src="image_219.png" /></figure>

* pseudonœuds et interactions tertiaires

<figure><img src="image_220.png" /></figure>

...

<figure><img src="image_221.png" /></figure>
RNA Puzzles

♦ tester les capacités de prédiction de structures 3D d'ARN

♦ compétition entre modélisateurs ARN

♦ compétition à “l’aveugle”: structures 3D d’ARN non publiques
# RNA Puzzle: T-Box/tRNA

* The T-box riboswitch in complex with tRNA

<figure><img src="image_222.png" /></figure>

* PDB: 4LCK

* Resolution: 3.20Å

* Avg B = 128 Å²

* tRNA: 75nt

* T-box: 96nt

* Clash score: 2.28

* Some small fragments solved by NMR before. tRNA structure known.
RNA Puzzle: T-Box/tRNA

<figure><img src="image_223.png" /></figure>
<table><caption>Table 1: Main tools offering a visualization of the RNA secondary structure.</caption><thead><tr><th>Name</th><th>Platform(s)<br>[BWML]</th><th>Ease of use</th><th>Layouts</th><th>Interactivity</th><th>Pseudoknots</th><th>Ext. sec. str.<sup>b</sup></th><th>Output<sup>c</sup></th><th>Reference</th></tr></thead><tbody><tr><td>jViz.RNA</td><td>●●●●</td><td>++</td><td>Circular<br>Linear<br>Graph</td><td>+</td><td>●</td><td></td><td>EPS PNG</td><td>(Wiese et al., 2005)<br>(Shabash et al., 2012)</td></tr><tr><td>PseudoViewer</td><td>●●○○</td><td>++</td><td>Graph</td><td>+</td><td>○</td><td></td><td>EPS SVG<br>PNG GIF</td><td>(Byun and Han, 2009)</td></tr><tr><td>RNA2DMap</td><td>●●●●</td><td>+</td><td>Graph</td><td>+</td><td>●</td><td></td><td>PDF<sup>e</sup></td><td>(Xu et al., 2011)</td></tr><tr><td>RNAMovies</td><td>●●●●</td><td>++</td><td>Graph</td><td>+</td><td>○</td><td></td><td>SVG PNG<br>JPEG GIF</td><td>(Kaiser et al., 2007)</td></tr><tr><td>R-chie</td><td>●●●●</td><td>++</td><td>Linear</td><td>+</td><td>○</td><td></td><td>PDF PNG</td><td>(Lai et al., 2012)</td></tr><tr><td>RNAPLOT</td><td>●<sup>d</sup>●●</td><td>+</td><td>Graph</td><td>○</td><td></td><td></td><td>PS SVG<br>GML</td><td>(Gruber et al., 2008)</td></tr><tr><td>RNAView</td><td>○●●●</td><td>+</td><td>Graph</td><td>+</td><td>●</td><td></td><td>PS</td><td>(Yang et al., 2003)</td></tr><tr><td>RNAViz</td><td>○●●●</td><td>+</td><td>Graph</td><td>++</td><td>○</td><td></td><td>PDF<sup>e</sup></td><td>(Rijk et al., 2003)</td></tr><tr><td>R2R</td><td>○●●●</td><td>-</td><td>Graph</td><td>+</td><td>○</td><td></td><td>PDF SVG</td><td>(Weinberg and Breaker, 2011)</td></tr><tr><td>S2S/Assemble</td><td>○●●●</td><td>+</td><td>Linear<br>Graph</td><td>++</td><td>●</td><td></td><td>SVG</td><td>(Jossinet and Westhof, 2005)<br>(Jossinet et al., 2010)</td></tr><tr><td>VARNA</td><td>●●●●</td><td>++</td><td>Circular<br>Linear<br>Graph</td><td>++</td><td>●</td><td></td><td>EPS SVG<br>PNG<br>JPEG<br>GIF</td><td>(Darty et al., 2009)</td></tr><tr><td>xRNA</td><td>○●●●</td><td>+</td><td>Graph</td><td>++</td><td>○</td><td></td><td>EPS</td><td>-</td></tr></tbody></table>

<sup>a</sup> Indicates presence (●) or absence (○) for Browser-based, Windows, Mac and Linux executions, in this order. <sup>b</sup> Indicates support (●) or lack of support (○) for an extended secondary structure.

<sup>c</sup> Bold output formats indicate vector graphics, allowing for convenient post-processing. <sup>d</sup> Only available from the Vienna RNA webserver, available at http://rna.tbi.univie.ac.at/. <sup>e</sup> Export accessible through a print option, using a custom printer driver such as Adobe Distiller.
Serveurs WEB généralistes:
ViennaRNA, BiBiServ, Freiburg RNA Tools
# ViennaRNA Web Services

## The ViennaRNA Web Services

This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server.

### Web Servers

#### Thermodynamic Structure Prediction

* RNAfold server...

...predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences.

* RNAalifold server...

...predicts *consensus* secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment.

* RNAeval server...

...provides a detailed thermodynamic description of a sequence/structure pair.

* RNAcofold server...

...allows you to predict the secondary structure of a dimer.

* RNAup server...

...allows you to predict the accessibility of a target region.

#### ncRNA Prediction

* Structure conservation analysis server...

...will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments.

* RNAz server...

...will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments.

* Bcheck...

...predicts rnpB genes.

* RNAstrand server...

...allows you to predict the reading direction of evolutionarily conserved RNA secondary structures.

### Folding Kinetics

* barriers server...

...allows you to get insights into RNA folding kinetics.

### Sequence Design

* RNAinverse server...

...allows you to design RNA sequences for any desired target secondary structure.

* RNAxs server...

...assists you in siRNA design.

### Genome Wide Screening

* RNApredator...

...predicts targets of small bacterial RNAs

* TSSAR...

...predicts bacterial Transcription Start Sites from dRNA-seq data.
# Freiburg RNA Tools

<figure><img src="image_224.png" /></figure>
<figure><img src="image_225.png" /></figure>

BiBiServ

Bielefeld University Bioinformatics Server

Tools

<figure><img src="image_226.png" /></figure>

Education

Administration

## Tools

Genome
Comparison

Gecko

REPuter

...more

Alignments

PoSSuMsearch2

ChromA

...more

Primer Design

GeneFisher2

RNA Studio

RNAsapes

KnotInFrame

RNAhybrid

...more

Evolutionary
Relationship

ROSE

...more

Others

XenDB

jPREditor

...more

## RNA Studio

* **GUUGle** GUUGle

A utility for fast exact matching under RNA base pairing rules

* **InSilicoDicer** Prediction of mature miRNA.

Intrinsic and Extrinsic Prediction of mature miRNA.

* **KnotInFrame** Prediction of -1 ribosomal frameshifts

KnotInFrame is a tool for predicting -1 ribosomal frameshifts with simple recursive pseudoknots as stimulating structural motif in mRNAs by means of the tool pknotsRG for the folding of the pseudoknots.

* **Locomotif** Localization of RNA motifs with generated thermodynamic Matchers

A graphical programming system for RNA motif search.

* **paRNAss** Prediction of Alternate RNA Secondary Structures

paRNAss is a software tool aiming to predict conformational switching in RNA.

* **pKiss**

pKiss is a tool for secondary structure prediction including kissing hairpin motifs.

* **pknotsRG** RNA folding and thermodynamic matching

pknotsRG is a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots.
# Bioinformatics Tools and Databases for Functional RNA Analysis

ncRNA.org is the portal site for bioinformatics tools and databases specialized for functional RNAs. The developments in this cite were partially supported by "The Functional RNA Project" funded by New Energy and Industrial Technology Development Organization (NEDO), Japan.

**Now Available!**

Results of various analysis on RNA secondary structures in one page!
Rtools

Accurate prediction of RNA secondary structure

CentroidFold

Prediction of RNA secondary structure by using homologous sequences

CentroidHomfold

Active Work Flow is available for RNA sequence/structure analysis.
You can download the Knime platform and the Active Work Flow for RNA structure predictions.
# CARNAC

## RNA tools

### DNA

YASS

Magnolia

mreps

ProCARs

### HTS

SortMeRNA

CRAC

Vidjil

SToRM

### RNA

Carnac

RNAfamily

Gardenia

Regliss

CG-seq

RNAspace

### Proteins

Path

Protea

ReBLOSUM

### TFM

TFM-Explorer

TFM-Scan

TFM-Pvalue

TFM-CUDA

### NRP

Norine

The RNA tools offer a series of bioinformatics program specifically designed for the analysis of structural RNA: secondary structure inference, alignment, annotation. unaligned

<figure><img src="image_227.png" /></figure>

<figure><img src="image_228.png" /></figure>

### Carnac

Predicts the consensus secondary structure for a set of homologous, unaligned RNA sequences. Very fast and accurate.

<figure><img src="image_229.png" /></figure>

### RNAfamily

Linear visualisation of RNA secondary structures

<figure><img src="image_230.png" /></figure>

### Gardenia

Comparison and multiple alignment of RNA sequences. The algorithm takes into account both the primary structure and the secondary structure to build a good alignment.

<figure><img src="image_231.png" /></figure>

### Regliss

This tools builds all locally optimal secondary structures of an RNA sequence, which provide a useful insight into the folding landscape of the molecule.

target sequence

CG-seq

predictions on
putative

noncoding RNAs
on the target
sequence

### CG-seq

It is a software pipeline to identify noncoding RNA genes in genomic sequences by comparative analysis and multispecies comparison.

<figure><img src="image_232.png" /></figure>

### RNAspace

Annotation platform for noncoding RNAs
Seveurs WEB:
structures 2D conservées
RNAalifold (Vienna)

<figure><img src="image_233.png" /></figure>
RNAfold

<figure><img src="image_234.png" /></figure>
**Standard
Analysis**

**Genomic
Screen**

**Help**

**Welcome to the RNAz web server.** It will help you to detect thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments.

Simply paste or upload your alignment(s) below and click Proceed. The system will suggest reasonable default values for all options. To get more information on the meaning of the options click the ? symbols or read the help pages. You can test the server using this sample alignment.

If you like to analyze alignments covering whole genomic regions use the *Genomic screen* modus.

Paste your alignment(s) here:

<figure><img src="image_235.png" /></figure>

[clear]

<figure><img src="image_236.png" /></figure>

Or upload a file:

<figure><img src="image_237.png" /></figure>

Choose File

no file selected

Format:

<figure><img src="image_238.png" /></figure>

Automatic

<figure><img src="image_239.png" /></figure>
# Banques de données
HOME | SEARCH | BROWSE |

FTP | BLOG | HELP

keyword search

Go

## Rfam 12.0 (July 2014, 2450 families)

The Rfam database is a collection of RNA families, each represented by **multiple sequence alignments, consensus secondary structures** and **covariance models (CMs)**. **More...**

**QUICK LINKS**

**SEQUENCE SEARCH**

**VIEW AN RFAM FAMILY**

**VIEW AN RFAM CLAN**

**KEYWORD SEARCH**

**TAXONOMY SEARCH**

**JUMP TO**

**YOU CAN FIND DATA IN RFAM IN VARIOUS WAYS...**

Analyze your RNA sequence for Rfam matches

View Rfam family annotation and alignments

View Rfam clan details

Query Rfam by keywords

Fetch families or sequences by NCBI taxonomy

enter any accession or ID

Go

Example

Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome

Or view the **help** pages for more information

**Recent Rfam **blog** posts**

Hide this

**Rfam 12.0 is out** (posted 24 September 2014)

We are pleased to announce the release of Rfam 12.0! This release contains some major changes when compared with previous releases of Rfam, so please take a minute to read our release notes. Rfam 12.0 is the first version of Rfam which is based on Infernal 1.1, and as such contains many significant changes. In [...]
## Family: snoR9 (RF00065)

**Description:** Small nucleolar RNA snoR9

12
sequences

0 species

0 structures

### Summary

### Summary

### Sequences

### Alignment

### Secondary structure

### Species

### Trees

### Structures

### Motif matches

### Database references

### Curation

### Jump to...

enter ID/acc

Go

### Wikipedia annotation

Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry entitled **Small nucleolar RNA snoR9**. You can see the Wikipedia page for this family here. More...

**snoR9** is a non-coding RNA (ncRNA) which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). It is known as a **small nucleolar RNA (snoRNA)** and also often referred to as a 'guide RNA'.

R9 is a member of the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs. [1]

This snoRNA was identified in a computational search for GC-rich regions in the AT-rich genomes of hyperthermophiles. [2] This snoRNA is not related to the plant snoRNA **snoR9**.

### Small nucleolar RNA snoR9

<figure><img src="image_240.png" /></figure>

<figure><img src="image_241.png" /></figure>

Predicted secondary structure and sequence conservation of snoR9

### References[edit]

1. ^ Galardi, S.; Fatica, A.; Bachi, A.; Scaloni, A.; Presutti, C.; Bozzoni, I. (October 2002). "Purified Box C/D snoRNPs Are Able to Reproduce Site-Specific 2'-O-Methylation of Target RNA in Vitro". Molecular and Cellular Biology **22** (19): 6663-6668.
doi:10.1128/MCB.22.19.6663-6668.2002
PMC 134041. PMID 12215523. edit

2. ^ Klein RJ, Misulovin Z, Eddy SR (2002). "Noncoding RNA genes identified in AT-rich hyperthermophiles". Proc. Natl. Acad. Sci. U.S.A. **99** (11): 7542-7.
doi:10.1073/pnas.112063799. PMC 124278.
PMID 12032319.

### Identifiers

Symbol snoR9

Rfam RF00065

### Other data

RNA type Gene; snRNA; snoRNA; CD-box

Domain(s) Archaea

GO 0006396 0005730

SO 0000593

### External links[edit]

- Page for Small nucleolar RNA snoR9 at Rfam

<figure><img src="image_242.png" /></figure>

This molecular or cell biology article is a stub. You can help Wikipedia by expanding it.

This page is based on a **wikipedia article**. The text is available under the **Creative Commons Attribution/Share-Alike License**.

# Rfam entry
RF00065

http://rfam.xfam.org
# Pseudobase

<figure><img src="image_243.png" /></figure>

Pseudobase

LEIDEN

Institute of

Theoretical

Biology

Leiden

Institute of

Chemistry

UNIVERSITY

A Pseudoknot Database

<figure><img src="image_244.png" /></figure>

<figure><img src="image_245.png" /></figure>

About PseudoBase

Retrieve by Class

Retrieve by Property

Submit Pseudoknots

## Intro

<figure><img src="image_246.png" /></figure>

## Welcome to PseudoBase

<figure><img src="image_247.png" /></figure>

PseudoBase is a collection of RNA pseudoknots that we make available for retrieval to the scientific community. It is described in detail in *Batenburg et al. (2000)*.

It started as an initiative of the Institute of Theoretical Biology and the Leiden Institute of Chemistry of the University of Leiden. For the future we intend to maintain it and to extend it.

This page is the main introduction from where you can depart to the **retrieval** section, to the **submit** section or to the **information** section.

<figure><img src="image_248.png" /></figure>

## Retrieve, Submit or more Info?

Please choose whether you want to retrieve a pseudoknot or submit a pseudoknot. If you need more information, you can choose the "About PseudoBase" option.

<figure><img src="image_249.png" /></figure>

About PseudoBase

Choose this option if you want to contact us, or if you need more information about us and about the PseudoBase project.

<figure><img src="image_250.png" /></figure>

Retrieve pseudoknot **by class** or **by summary**

Choose either of these options to retrieve a particular pseudoknot. The "by class" page

presents all pseudoknots organised by their class. The "by summary" page presents all pseudoknots in a table that you can sort to your taste. Sorting criteria are among others: class, name, organism and length of pseudoknot stems and loops.

<figure><img src="image_251.png" /></figure>

Submit a new pseudoknot to PseudoBase

Choose this option for the section where you can submit a pseudoknot.

<figure><img src="image_252.png" /></figure>

<figure><img src="image_253.png" /></figure>
RNAcentral

http://rnacentral.org

RNAcentral is a new resource
that provides unified access to
the ncRNA sequence data
supplied by the Expert
Databases. Learn more (/about-us)

<figure><img src="image_254.png" /></figure>

(/expert-
database/refseq)

**RefSeq** is a
comprehensive,
integrated, non-
redundant, well-
annotated set of
reference sequences.
**30,900** sequences
(example
(/rna/URS000075A3E5
))

Explore RefSeq entries (/expert-database/refseq)

<figure><img src="image_255.png" /></figure>

ENA

(/expert-
database/ena)

ENA provides a
comprehensive record of
the world's nucleotide
sequencing information.
**6,989,739** sequences
(example
(/rna/URS00002D0E0C
)))

Explore ENA entries (/expert-database/ena)

<figure><img src="image_256.png" /></figure>

Rfam

(/expert-
database/rfam)

Rfam is a database
containing information
about ncRNA families
and other structured
RNA elements.
**2,493,782** sequences
(example
(/rna/URS00000478B7
)))

Explore Rfam entries (/expert-database/rfam)

<figure><img src="image_257.png" /></figure>

(/expert-
database/vega)

**Vega** is a repository for
high-quality gene
models produced by the
manual annotation of
vertebrate genomes.
Human and mouse data
from Vega are merged
into GENCODE.
**28,640** sequences
(example
(/rna/URS00000B15DA
)))

Explore Vega entries (/expert-database/vega)

<figure><img src="image_258.png" /></figure>

(/expert-
database/gtrnadb)

**gtRNAb** contains tRNA
gene predictions on
complete or nearly
complete genomes.
**10,625** sequences
(example
(/rna/URS000047C79B
)))

Explore gtRNAb entries (/expert-database/gtrnadb)

<figure><img src="image_259.png" /></figure>

(/expert-
database/mirbase)

**miRBase** is a database
of published miRNA
sequences and
annotations that
provides a centralised
system for assigning
names to miRNA genes.
**8,795** sequences
(example
(/rna/URS00000478B7
)))

Explore miRBase entries (/expert-database/mirbase)

Explore miRBase entries (/expert-database/mirbase)

<figure><img src="image_260.png" /></figure>

(/expert-
database/rdp)

**RDP** provides quality-
controlled, aligned and
annotated rRNA
sequences and a suite of
analysis tools.
**4,779** sequences
(example
(/rna/URS000064300F
)))

Explore RDP entries (/expert-database/rdp)

<figure><img src="image_261.png" /></figure>

(/expert-
database/tmrna-
website)

**tmRNA Website**
contains predicted
tmRNA sequences from
RefSeq prokaryotic
genomes, plasmids and
phages.
**2,857** sequences
(example
(/rna/URS000060F5B3
)))

Explore tmRNA Website entries (/expert-database/tmrna-website)

<figure><img src="image_262.png" /></figure>

(/expert-
database/srpdb)

SRPDB provides
aligned, annotated and
phylogenetically ordered
sequences related to
structure and function of
SRP.

**503** sequences
(example
(/rna/URS00000478B7
)))

Explore SRPDB entries (/expert-database/srpdb)

<figure><img src="image_263.png" /></figure>

(/expert-
database/Incrnadb)

**IncRNAb** is a database
providing comprehensive
annotations of
eukaryotic long non-
coding RNAs (IncRNAs).
**62** sequences
(example
(/rna/URS00000478B7
)))

Explore IncRNAb entries (/expert-database/incrnadb)
<figure><img src="image_264.png" /></figure>

THE UNIVERSITY OF TEXAS AT AUSTIN

COMPARATIVE RNA WEB SITE AND PROJECT

THE GUTELL LAB

Welcome to the Comparative RNA Web (CRW) Site.

Recent CRW Site Publications
(Complete List »)

**2014:** **(Pub #129)** Multiple entries in: Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition, Hancock J.M. and Zvelebil M.J. (eds.). Wiley. Hoboken, New Jersey.

**2014:** **(Pub #128)** Ten Lessons with Carl Woese about RNA and Comparative Analysis. RNA Biology, in press.
[ **PM** | **pmc** | **DOI** ]

**2014:** **(Pub #127)** Introduction to Special Carl Woese Issue in RNA Biology. RNA Biology, 11(3):170-171. [ pm | pmc | DOI ]

**2014:** **(Pub #126)** Helix Capping in RNA Structure. PLOS One, 9(4):e93664. [ **PM** | **PMC** | **DOI** ]

**2013:** **(Pub #125)** *Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems*. BMC Systems Biology, 7(S4):S13. [ pm | pmc | DOI ]

**2013:** **(Pub #124)** You tell Carl that some of my best friends are Eukaryotes: Carl R. Woese (1928-2012). RNA 19(4):vii-xi.
[ pm | pmc | doi ]

**2013:** **(Pub #123)** Specificity between Lactobacilli and Hymenoptera Hosts is the Exception Rather than the Rule. Applied and Environmental Microbiology, 79:1803-1812. [ **PM** | **pmc** | **DOI** ]

**2013:** **(Pub #122)** Comparative Analysis of the Higher-Order Structure of RNA. In: *Biophysics of RNA Folding* ("Biophysics for the Life Sciences" Series). pp. 11-22. Springer, New York, NY. [ pm | pmc | DOI ]

**2012:** **(Pub #121)** *An Accurate Scalable Template-based Alignment Algorithm*. Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. pp. 237-243.
[ **PM** | **PMC** | **DOI** ]

**2012:** **(Pub #120)** *The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum*. PLoS One, 7(6):e38320.
[ **PM** | **PMC** | **DOI** ]

**2012:** **(Pub #119)** *Structural Constraints Identified with Covariation Analysis in Ribosomal RNA*. PLoS One, 7(6):e39383.
[ **PM** | **PMC** | **DOI** ]

**2012:** **(Pub #118)** *A Comparison of the Crystal Structures of the Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions*. PLoS One, 7(5):e38203. [ **PM** | **PMC** | **DOI** ]

**2011:** **(Pub #117)** *rCAD: A Novel Database Schema for the Comparative Analysis of RNA*. 7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp. 15-22. [ **PM** | **PMC** | **DOI** ]
# Serveur d'annotation
d'ARNnc
RNAspace

Home

1. Load data

2. Predict

3. Explore

HELP

Welcome to RNAspace

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation.

The increasing number of ncRNA discovered since 2000 and the lack of user friendly tools for finding and annotating them, have made necessary to propose to biologists an *in silico* environment allowing structural and functional annotations of these molecules with regard to available protein genes annotation environments.

RNAspace makes available a variety of **ncRNA gene finders** and **ncRNA databases** as well as user-friendly tools to explore computed results including comparison, visualization and edition of putative RNAs. RNAspace also allows to export putative RNAs in various **formats**.

<figure><img src="image_265.png" /></figure>

Partners

<figure><img src="image_266.png" /></figure>

FAQ

<figure><img src="image_267.png" /></figure>

Contact

Availability

RNAspace is an open source project. It is developed in Python. It is copyrighted with the GNU General Public License, and is free (in the GNU sense) for all to use, and is in constant development. RNAspace is hosted at Sourceforge. It is also available as a web server at rnaspace.org.

News

June 28, 2013 The site is now running on a new and more powerful computer environment provided by the Genotoul Bioinformatics platform with a reduced list of Infernal models.

RNAspace software v1.2.1 (July 28, 2011) is running
this site.

<figure><img src="image_268.png" /></figure>

Comments and remarks: contact@rnaspace.org.

http://www.rnaspace.org
Autres outils:
représentation
# VARNA: Visualization Applet for RNA

A Java lightweight component and applet for drawing the RNA secondary structure

Home

Demo

User Manual

Tutorials

Downloads

Java Security Fix

Links

## Announcement

VARNA 3.91 released

08/09/2014

Bulging loops, angular

hysteresis...

## Support

ANR

<figure><img src="image_269.png" /></figure>

LIX

<figure><img src="image_270.png" /></figure>

LIX, Palaiseau

LRI, Orsay

<figure><img src="image_271.png" /></figure>

<figure><img src="image_272.png" /></figure>

Polytechnique,
Palaiseau

IGM,
Orsay

<figure><img src="image_273.png" /></figure>

UNIVERSITÉ
PARIS-SUD 11

Recent changes in Java security policy might prevent you from running VARNA.

Check out this page for details and ways to solve the problem.

## What VARNA is

### Description

VARNA is Java lightweight Applet dedicated to **drawing the secondary structure of RNA**. It is also a Swing component that can be very easily included in an existing Java code working with RNA secondary structure to provide a fast and interactive visualization.

Being **free of fancy external library dependency** and/or network access, the VARNA Applet can be used as a base for a standalone applet. It looks reasonably good and **scales up or down nicely** to adapt to the space available on a web page, thanks to the anti-aliasing drawing primitives of Swing.

### Motivation

The initial version was coded after several unfruitful attempts at finding a RNA secondary structure drawing software to be used inside of a webserver. Indeed, it seemed at the time that most of the webservers dedicated to the secondary structure of RNA offered rather clumsy renderings (Mostly *static*, cgi-bin generated, PS or PNG files).

In 2008, I (Yann Ponty) was unable to find a tool that would be at the same time available, easy to install and still running (SStructView was no longer tolerated by latest Java plugins security policies; RNAMLView's goal was rather to display a projection of the 3D structure, and RNAMovies was more tailored towards animations...). Therefore, I coded a basic software *from scratch*, initially using a *radial* layout strategy adopted by the software RNAViz, later to be extended to other classic algorithms such that *NAView*, a classic Feynman-diagram representation and a linear one, hoping it would be useful to some... VARNA development team was subsequently joined by Kevin Darty and Alain Denise (LRI/IGM-Orsay-France) in 2009, leading to a complete redesign of the software.

As of November 2012, VARNA is currently used by RNA scientists and websites such as the NestedAlign web server, the IRESite database (Example), and the TFold webserver.

Biogeeks also features (featured?) a very nice tutorial showing how to use VARNA as a front end to RNAFold through a minimal Ruby script.

## Credits/License/Disclaimer

If you find VARNA useful to your research, please contribute to its continued development by citing its supporting manuscript:

VARNA: Interactive drawing and editing of the RNA secondary structure

Kévin Darty, Alain Denise and Yann Ponty

Bioinformatics, pp. 1974-1975, Vol. 25, no. 15, 2009
R-Chie

R-chie [arči]

A web server and R package for plotting arc diagrams of RNA secondary structures

* Home (index.cgi)

* Create a Plot (plot.cgi)

* FAQ (faq.cgi)

* Citation (cite.cgi)

* Download (download.cgi)

* Rfam Gallery (rfam.cgi)

**R-chie** allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding multiple sequence alignments and co-variation information.

**R4RNA** is the R package powering R-chie, available for [download (download.cgi)](https://www.e-rna.org/r-chie/plot.cgi) and local use for more customized figures and scripting.

Available types of plots (click to load example input to web form)

Single Structure (plot.cgi?eg=single)

Double Structures (plot.cgi?eg=double)

Overlapping Structures (plot.cgi?eg=overlap)

Single Covariance (plot.cgi?eg=singlecov)

Double Covariance (plot.cgi?eg=doublecov)

Overlapping Covariance (plot.cgi?eg=overlapcov)

<figure><img src="image_274.png" /></figure>

(plot.cgi?eg=single)

Visualize complicated basepairing as arcs on a linear sequence, colouring basepairs by value.

e.g. TRANSAT (cite.cgi) basepairs predictions for the Cripavirus internal ribosomal entry site (IRES), RF00458, coloured by p-value.
## RILogo - web server

Submit

Help & Download

RILogo creates RNA-RNA interaction logos for two RNAs. The input are either two single sequences or two multiple sequence alignments with annotation of intra- or intermolecular base pairing between the two RNAs. RILogo displays sequence conservation by a sequence logo for each RNA and structure conservation by the mutual information of the secondary structure base pairings. RILogo supports four different methods for calculating the mutual information.

See the Help page for input formats and examples. RILogo is free of charge and also available for download as an open source standalone program.

<figure><img src="image_275.png" /></figure>

## Submit

Please fill out the submission form and click the Submit button. Input fields marked with a * are required. (Load Example Data)

### Multiple Sequence Alignment*

Enter your multiple sequence alignment with structure annotation here. Either use the text area or upload a file.

Supported formats are Stockholm, Clustal or Fasta.

In Clustal and Fasta format, the secondary structure annotation must have the sequence name *structure*.

The alignment can also contain both interacting RNAs.

In that case, both sequences belonging to one species must be separated by the ' & ' character. [?]

<figure><img src="image_276.png" /></figure>

Upload alignment file:

Choose File

no file selected

### 2nd Multiple Sequence Alignment

If the first alignment contains only one RNA, then insert the second alignment here. Either use the text area or upload a file. [?]

<figure><img src="image_277.png" /></figure>

Upload alignment file:

Choose File

no file selected

### Mutual Information measure:

<figure><img src="image_278.png" /></figure>

RILogo implements four different measures for the mutual information of base pairs.

Please refer to the paper for the exact definitions. [?]

Submit
RNAfdl

Description ▼

Downloads (/projects/sfnet_rnafdl/releases/)

SourceForge.net page (http://sourceforge.net/projects/rnafdl)

Project Description

<figure><img src="image_279.png" /></figure>

Image list (/projects/sfnet_rnafdl/images/)

RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, line plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings.

(This Description is auto-translated)

Try to translate to Japanese (/projects/sfnet_rnafdl/translate/)

Show Original Description

Write Howto Install (/projects/sfnet_rnafdl/howto/install)

Write Howto Use (/projects/sfnet_rnafdl/howto/usage)

Download

Latest Files

RNAfdl-1.08.tar.gz (/projects/sfnet_rnafdl/downloads/RNAfdl-1.08.tar.gz/) (Date: 2014-08-19, Size: 871.0 KB)

RNAfdl-1.07.tar.gz (/projects/sfnet_rnafdl/downloads/RNAfdl-1.07.tar.gz/) (Date: 2014-08-07, Size: 895.8 KB)

RNAfdl-1.06.tar.gz (/projects/sfnet_rnafdl/downloads/RNAfdl-1.06.tar.gz/) (Date: 2014-08-02, Size: 900.7 KB)

RNAfdl-1.05.tar.gz (/projects/sfnet_rnafdl/downloads/RNAfdl-1.05.tar.gz/) (Date: 2014-01-01, Size: 763.7 KB)

RNAfdl-1.04.tar.gz (/projects/sfnet_rnafdl/downloads/RNAfdl-1.04.tar.gz/) (Date: 2013-08-20, Size: 760.7 KB)

<figure><img src="image_280.png" /></figure>

Download File List (/projects/sfnet_rnafdl/releases/)
# Ralee (emacs)

What does it look like?

<figure><img src="image_281.png" /></figure>

Using RALEE mode in GNU Emacs to edit an alignment of some U1 spliceosomal RNA sequences. The secondary structure base pairing pattern is annotated as nested pairs of < and > symbols. Bases of the same colour are part of the same helix. The split-screen view allows editing of base paired regions of the alignment even if they are far apart in sequence. For instance, the yellow bases in the top panel pair with the yellow bases in the bottom panel.

http://sgjlab.org/ralee/
<figure><img src="image_282.png" /></figure>

RnaViz

Welcome to the homepage of RnaViz

Documentation

Guided tour

Binary distributions

Source distribution

## Latest News

2013 Dec.: an easier binary distribution is available (this includes all dependencies)

## What is RnaViz

RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. Display of special structural elements such as pseudo-knots or unformatted areas is possible. Sequences can be automatically numbered, and several other types of labels can be used to annotate particular bases or areas. Although the program does not try to produce an initially non-overlapping drawing, the layout of a properly positioned structure drawing can be applied to newly created drawing using skeleton files. In this way a range of similar structures can be drawn with a minimum of effort. Skeletons for several types of RNA molecule are included with the program.

Some of the features

* recognises ct, rnaml and DCSE alignment formats

* multiple structures on page

* simple but powerfull WYSIWYG editing using different selection modes

* skeletons to easily draw many structure using the same layout

* allows display of pseudoknots

* free choice of fonts, colors, linewidths for any object

* graphica objects for annotation (rectangle, oval, lines, text)

* linking of graphics, text to certain bases

* tag based changing of properties

* automatic sequence numbering

* zoom

* independent scaling of structure drawings

* portable
Autres outils:
prédictions
RNA TOOLS: RNAbows, BINDIGO, and PSR

<figure><img src="image_283.png" /></figure>

**RNAbows** present intuitive visualization of RNA base pairing probabilities.

BINDING
| | | |
OLIGO

**BINDIGO** is a new, faster algorithm to calculating optimal binding of oligometric RNA to an RNA target.

PRIMARY
SEQUENCE
RANK

<figure><img src="image_284.png" /></figure>

RRREEE
AANN
PSQIMUCKY

**PSR** is an algorithm for efficiently discriminating donor splice sites from decoy sequences.
RNAbows

We offer three types of RNAbows for visualizing partition function computations.

<figure><img src="image_285.png" /></figure>

AllPairs

Base pairs are denoted by arcs whose thickness and shade is proportional to their probability.

<figure><img src="image_286.png" /></figure>

Clusters

After splitting the partition function, the two dominant clusters of folds are compared.

<figure><img src="image_287.png" /></figure>

diffRNAbow
diffRNAbow

Highlights differences between the folds of two sequences of the same length.

http://rna.williams.edu/rnabows/
RNAmutants

Exploring the effects of mutations on the secondary structure of RNAs

Home

News

Download

Webserver

FAQs

Tutorial

References

Contact

<figure><img src="image_288.png" /></figure>

**Keywords:** thermostability, beneficial and deleterious mutations, thermodynamic pressure, RNA design, evolution.

**More details? Visit the FAQs.**
Autres outils:
2D & 3D
Structures 2D & 3D

<figure><img src="image_289.png" /></figure>
# BGSU RNA bioinformatics

## BGSU RNA STRUCTURAL BIOINFORMATICS

Bowling Green State University (/) / Research (//www.bgsu.edu/research.html) / BGSU RNA Structural Bioinformatics

<figure><img src="image_290.png" /></figure>

### Structural Databases

RNA 3D Hub (http://rna.bgsu.edu/rna3dhub) is a new resource, which contains:

* RNA 3D Motif Atlas (http://rna.bgsu.edu/rna3dhub/motifs), a representative collection of RNA 3D motifs.

* Non-redundant lists (http://rna.bgsu.edu/rna3dhub/nrlist) of RNA-containing 3D structures.

http://www.bgsu.edu/research/rna/
<figure><img src="image_291.png" /><figcaption>Secondary Structure: small subunit ribosomal RNA</figcaption></figure>

Escherichia coli

(J01695)

1.cellular organisms 2.Bacteria 3.Proteobacteria

4.gamma subdivision

5. Enterobacteriaceae and related symbionts

6. Enterobacteriaceae 7. Escherichia
November 1999 (cosmetic changes July 2001)

Symbols Used In This Diagram:

G — C • Canonical base pair (A-U, G-C)

G • U - G-U base pair

G o A - G-A base pair

U • U - Non-canonical base pair

Every 10th nucleotide is marked with a tick mark,
and every 50th nucleotide is numbered.

Tertiary interactions with strong comparative data are connected by solid lines.