vizbi2013: visualising rna

Visualising RNA

Paul [email protected]

University of Canterbury, Christchurch,New Zealand.

March 20, 2013

Paul Gardner Visualising RNA

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What is an RNA?

GCGGAUUU

AGCUC

AGDDGG G A

G A G CG

CCA

GACUG

A A.A.

CUGGAGGU

CC U G U G

T . CGA

UCCACAG

AAUUCGC

AC

CA

VariableLoopAnticodon

Loop

T ΨCLoop

10 15 20 25 30 355 40 45 50 55 60 65 70 75

AnticodonLoop

Acceptor Stem

GCGGAUUUAGCUCAGDDGGGAGAGCGCCAGACUGAAYA.CUGGAGGUCCUGUGT.CGAUCCACAGAAUUCGCACCA5’ 3’

Secondary Structure Tertiary StructureB C

Primary StructureA

Acceptor Stem

T ΨCLoop

ΨΨ

Ψ

Ψ

Y

6560

55

40

10

20

155

70

75

25

30

35

45

50

D Loop

3’

5’

5’3’

D Loop


What is Rfam?

I Sister database to Pfam

I Aims to annotate all ncRNA families

I Consortium headed by Alex Bateman (Wellcome Trust SangerInstitute), Sean Eddy (Janelia, Howard Hughes), SamGriffiths-Jones (Manchester, BBSRC), Paul Gardner(University of Canterbury, RSNZ)


Rfam: families of ncRNAs

http://rfam.sanger.ac.ukhttp://rfam.janelia.org


Building an Rfam family

I A structure from literature

Pollard KS, et al. (2006). An RNA gene expressed during cortical development evolved rapidly in humans. Nature.



I An Rfam family: produced manually from publication figures# STOCKHOLM 1.0

G.gallus.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUAGM.musculus.1 UAAAAUGGAGGAGAAAUUACAGCAAUUUAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCCGUGGM.mulatta.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGG.gorilla.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGH.sapiens.1 UGAAACGGAGGAGACGUUACAGCAACGUGUCAGCUGAAAUGAUGGGCGUAGACGCACGUCAGCGGCGGP.troglodytes.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGP.abelii.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGC.lupus.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCGGUGCT.truncatus.1 CGAAAAGGAGGGGAAAUUACAGCAAUUCAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGB.taurus.1 CGAAAUGGAGGAGAAAUUACAGCAAUUCAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGV.pacos.1 UGAAACAGAGGAGAAAUUACAGCAAUUCAUCAACCGAAAUGAUAGGGAUAGACAUGUGUCGGCAGUGGM.lucifugus.1 CGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAUCCGUGGO.anatinus.1 UGAAAUGGAGGAUAAAUUACAGCAAUUUAUCAAAUGAAAUUAUAGGUGUAGACACAUGUCAGCAAUGG#=GC SS_cons <<<<<<.<<<<<<<<<<<.....>>>>>.....>><<<<<.<<<.<<<....>>>.>>>.........#=GC RF uGaaacGGaGGagaaguuAcAGcaacuuAUcAgcuGaaacuaugGGcGUAGACgCAcgucAGcaguGg

G.gallus.1 AAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCAM.musculus.1 AAAUGGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCAM.mulatta.1 AAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCAG.gorilla.1 AAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCAH.sapiens.1 AAAUGGUUUCUAUCAAAAUGAAAGUGUUUAGAGAUUUUCCUCAAGUUUCAP.troglodytes.1 AAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCAP.abelii.1 AAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCAC.lupus.1 AAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCAT.truncatus.1 GAACACUUUCUAUCAAAAUUAAAGUACUUAGCGAUUUUCCUUAAAUUUCAB.taurus.1 AAACCGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUUAAAUUUCAV.pacos.1 AAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGACUUUCCUCAAAUUUCAM.lucifugus.1 AAACAGUUACGAUCAAAAUUAAAGUGUUUAGAGAUUUUCCUC.AAUUUUAO.anatinus.1 AAACAAUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA#=GC SS_cons .....>>>>>....<<<<<..............>>>>>>>>>..>>>>>>#=GC RF AAAuaguuuCUAUcaaaauuAAAGUAUUUAGAGauuuuCCuCAAguuuCa//



I And the Wikipedia entry


Conflicting priorities

I A Curator’s priorities

1. New families2. Accuracy of models3. Annotation4. Functional codebase5. Website6. Visualization

I A User’s priorities

1. FTP (Bioinformaticians)2. Website3. Visualization4. Number of families5. Accuracy of models6. Annotation

Image credits: www.conflictdynamics.org


http://www.conflictdynamics.org/blog/wp-content/uploads/2011/11/AngerConflict.jpg

2007: challenges

I Quality ControlI Re-write the website and add some blingI Update codebaseI Export annotation to WikipediaI User community input via RNA Biology


Visualisation priorities

SCALEI Two to two million sequences, 30 to 3,000 nucleotides long, 0

to 1,000 basepairs.

I AUTOMATED: thousands of families.

INFORMATIVEI Generates biologically relevant hypotheses

INCLUSIVEI Make the most of our fantastic Bioinformatic & Visualisation

community.


Examples

I Caveat: none of these images I am showing are final solutions,everything can be improved upon.

I Secondary Structure

I Taxonomic Distribution

I Alignment

I Genomic contexts & GeneOrder


RNA Secondary Structure

5’ 3’

0Sequence conservation

1

UVDWHAUGAUGA

GY

UC

MACUUCWUuGG

UC

CG U G U U U C U G A g a R MCYM

RUGAUMUBWRU

Ga

SA

AaGUUCUGAY

UHM

Gardner, Bateman & Poole (2010) SnoPatrol: how many snoRNA genes are there?. Journal of Biology.


http://jbiol.com/content/9/1/4

Old Taxonomic distributions: RybB

I Contamination displayed first.


Old Taxonomic distributions: RybB

I After some scrolling


New Taxonomic distributions: RybBI Sunbursts: concentric “pie charts”, each external ring

contains the “children” nodes of the internal ring.


Alignments

I When we have sequenced everything, how is this view goingto look?


Genomic contexts & Gene Order

I How can we display comparative gene-order information in ascalable fashion?

I Think of hundreds to thousands of genomes, tens to hundredsof features.

Barquist L, et al. (2013). A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and

Typhimurium. Nucleic Acids Research.


Open problems

I Evolution and RNA structureI Scalable, alignment visualisation (and editing)

I As alignments grow, we need to be able to be able to partition,compress and summarize groupings of sequences. 1,000s ofsequences from the same species is not interesting to view, noris a screen full of gaps.

I Expression and conservation levels

I Genomic context & gene-order


Thanks!

I The Rfam Consortium:I Alex Bateman, Sean

Eddy, SamGriffiths-Jones, SarahBurge, Eric Nawrocki,John Tate, Rob Finn,Jennifer Daub, RuthEberhardt

I Visualisation Tools:I Ivo Hofacker, Yann

Ponti, Jim Proctor,Ian Holmes, IrmtraudMeyer, ZashaWeinberg and manyothers.

PPG is supported by a Rutherford Discovery Fellowship from Government funding, administered by the RoyalSociety of New Zealand.


vizbi2013: visualising rna

Technology

visualising rna paul

paul gardnervisualising

rna structurescalable

c gagg55 c g

rna secondary structure5

gacacg g cugug g g g

loopacceptor c gstem

yaus c