The document discusses visualizing RNA structures and sequences. It provides background on RNA families database Rfam and the process of building RNA families from literature and annotation. It also touches on priorities for RNA visualization tools, including scale, informativeness, and inclusiveness, and provides some example visualizations like secondary structure, alignment, taxonomic distribution, and genomic context. Conflicting priorities between curators and users are noted. Challenges in 2007 around quality control, the website, codebase, and community input are outlined.

1. Visualising RNA
Paul Gardner
paul.gardner@canterbury.ac.nz
University of Canterbury, Christchurch,
New Zealand.
March 20, 2013
Paul Gardner Visualising RNA

2. Feel free to share
Feel free to tweet (@ppgardne), Google+, tumblr, ...
Slides are available from
http://www.slideshare.net/ppgardne/.
Paul Gardner Visualising RNA

3. What is an RNA?
A Primary Structure
5 10 15 20 25 30 35 40 45 50 55 60 65 70 75
Ψ Ψ
5’ GCGGAUUUAGCUCAGDDGGGAGAGCGCCAGACUGAAYA.CUGGAGGUCCUGUGT.CGAUCCACAGAAUUCGCACCA 3’
B Secondary Structure C Tertiary Structure
75
3’A C 5’
C T ΨC 3’
5’ G C A Loop
Acceptor C G
Stem G C 70
GU T ΨC
D Loop 5A U Acceptor
15 UA Loop D Loop
DGA U U A 65 60 Stem
D A C UA
C U C G 10 GACAC
G G CUGUG G
G G A A G C 25 C 50
G U T ΨC
.
20
C GAG G 55
C G 45
AU
G C 40
A 30
C Ψ . Variable
Anticodon U A Anticodon
Loop
Loop G
A A
.
Y Loop
35
Paul Gardner Visualising RNA

4. What is Rfam?
Sister database to Pfam
Aims to annotate all ncRNA families
Consortium headed by Alex Bateman (Wellcome Trust Sanger
Institute), Sean Eddy (Janelia, Howard Hughes), Sam
Griffiths-Jones (Manchester, BBSRC), Paul Gardner
(University of Canterbury, RSNZ)
Paul Gardner Visualising RNA

5. Rfam: families of ncRNAs
http://rfam.sanger.ac.uk
http://rfam.janelia.org
Paul Gardner Visualising RNA

6. Building an Rfam family
A structure from literature
Pollard KS, et al. (2006). An RNA gene expressed during cortical development evolved rapidly in humans. Nature.
Paul Gardner Visualising RNA

7. Building an Rfam family
An Rfam family: produced manually from publication figures
# STOCKHOLM 1.0
G.gallus.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUAG
M.musculus.1 UAAAAUGGAGGAGAAAUUACAGCAAUUUAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCCGUGG
M.mulatta.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGG
G.gorilla.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGG
H.sapiens.1 UGAAACGGAGGAGACGUUACAGCAACGUGUCAGCUGAAAUGAUGGGCGUAGACGCACGUCAGCGGCGG
P.troglodytes.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGG
P.abelii.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGG
C.lupus.1 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCGGUGC
T.truncatus.1 CGAAAAGGAGGGGAAAUUACAGCAAUUCAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGG
B.taurus.1 CGAAAUGGAGGAGAAAUUACAGCAAUUCAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGG
V.pacos.1 UGAAACAGAGGAGAAAUUACAGCAAUUCAUCAACCGAAAUGAUAGGGAUAGACAUGUGUCGGCAGUGG
M.lucifugus.1 CGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAUCCGUGG
O.anatinus.1 UGAAAUGGAGGAUAAAUUACAGCAAUUUAUCAAAUGAAAUUAUAGGUGUAGACACAUGUCAGCAAUGG
#=GC SS_cons <<<<<<.<<<<<<<<<<<.....>>>>>.....>><<<<<.<<<.<<<....>>>.>>>.........
#=GC RF uGaaacGGaGGagaaguuAcAGcaacuuAUcAgcuGaaacuaugGGcGUAGACgCAcgucAGcaguGg
G.gallus.1 AAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
M.musculus.1 AAAUGGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
M.mulatta.1 AAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
G.gorilla.1 AAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
H.sapiens.1 AAAUGGUUUCUAUCAAAAUGAAAGUGUUUAGAGAUUUUCCUCAAGUUUCA
P.troglodytes.1 AAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
P.abelii.1 AAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
C.lupus.1 AAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
T.truncatus.1 GAACACUUUCUAUCAAAAUUAAAGUACUUAGCGAUUUUCCUUAAAUUUCA
B.taurus.1 AAACCGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUUAAAUUUCA
V.pacos.1 AAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGACUUUCCUCAAAUUUCA
M.lucifugus.1 AAACAGUUACGAUCAAAAUUAAAGUGUUUAGAGAUUUUCCUC.AAUUUUA
O.anatinus.1 AAACAAUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
#=GC SS_cons .....>>>>>....<<<<<..............>>>>>>>>>..>>>>>>
#=GC RF AAAuaguuuCUAUcaaaauuAAAGUAUUUAGAGauuuuCCuCAAguuuCa
//
Paul Gardner Visualising RNA

8. Building an Rfam family
And the Wikipedia entry
Paul Gardner Visualising RNA

9. Conflicting priorities
A Curator’s priorities A User’s priorities
1. New families 1. FTP (Bioinformaticians)
2. Accuracy of models 2. Website
3. Annotation 3. Visualization
4. Functional codebase 4. Number of families
5. Website 5. Accuracy of models
6. Visualization 6. Annotation
Image credits: www.conflictdynamics.org
Paul Gardner Visualising RNA

10. 2007: challenges
Quality Control
Re-write the website and add some bling
Update codebase
Export annotation to Wikipedia
User community input via RNA Biology
Paul Gardner Visualising RNA

11. Visualisation priorities
SCALE
Two to two million sequences, 30 to 3,000 nucleotides long, 0
to 1,000 basepairs.
AUTOMATED: thousands of families.
INFORMATIVE
Generates biologically relevant hypotheses
INCLUSIVE
Make the most of our fantastic Bioinformatic & Visualisation
community.
Paul Gardner Visualising RNA

12. Examples
Caveat: none of these images I am showing are final solutions,
everything can be improved upon.
Secondary Structure Alignment
Taxonomic Distribution Genomic contexts & Gene
Order
Paul Gardner Visualising RNA

13. RNA Secondary Structure
5’ 3’
UM
VH
DU
UA HWY A GU
AG CU
U U
G G
A a
G A
Y A
U S
C a
M G
A U
C R
U W
U B
C U
W M
U U
u A
G G
G U
U R
C M
C Y
G C
U M
GU R
UUCUGA g a
0 1
Sequence conservation
Gardner, Bateman & Poole (2010) SnoPatrol: how many snoRNA genes are there?. Journal of Biology.
Paul Gardner Visualising RNA

14. Old Taxonomic distributions: RybB
Contamination displayed first.
Paul Gardner Visualising RNA

15. Old Taxonomic distributions: RybB
After some scrolling
Paul Gardner Visualising RNA

16. New Taxonomic distributions: RybB
Sunbursts: concentric “pie charts”, each external ring
contains the “children” nodes of the internal ring.
Paul Gardner Visualising RNA

17. Alignments
When we have sequenced everything, how is this view going
to look?
Paul Gardner Visualising RNA

18. Genomic contexts & Gene Order
How can we display comparative gene-order information in a
scalable fashion?
Think of hundreds to thousands of genomes, tens to hundreds
of features.
Barquist L, et al. (2013). A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and
Typhimurium. Nucleic Acids Research.
Paul Gardner Visualising RNA

19. Open problems
Evolution and RNA structure
Scalable, alignment visualisation (and editing)
As alignments grow, we need to be able to be able to partition,
compress and summarize groupings of sequences. 1,000s of
sequences from the same species is not interesting to view, nor
is a screen full of gaps.
Expression and conservation levels
Genomic context & gene-order
Paul Gardner Visualising RNA

20. Thanks!
The Rfam Consortium:
Alex Bateman, Sean
Eddy, Sam
Griffiths-Jones, Sarah
Burge, Eric Nawrocki,
John Tate, Rob Finn,
Jennifer Daub, Ruth Visualisation Tools:
Eberhardt Ivo Hofacker, Yann
Ponti, Jim Proctor,
Ian Holmes, Irmtraud
Meyer, Zasha
Weinberg and many
others.
PPG is supported by a Rutherford Discovery Fellowship from Government funding, administered by the Royal
Society of New Zealand.
Paul Gardner Visualising RNA