Download Roland Schwarz - BiVi AGM

Joint visualisation and analysis of large sequence data
with Alvis and Sequence Bundles
Roland F Schwarz
Science meets design
Science
Practice
2013 redesign competition
http://www.ebi.ac.uk/goldman-srv/sequencebundles/
Multiple sequence alignments
• Phylogenetics
• Protein
function
annotation
• Structure
prediction
• Motif detection
• …
Most visualisations are aggregative
• High-dimensional
• Hard to interpret by eye
• Traditional methods of visualization are
aggregative across rows or columns
• Insufficient representation of the
information content of the MSA
Sequence Bundles
• Sequences rendered as semi-opaque
Bezier curves
• Displayed on a grid alphabet size x
alignment length
• Non-aggregative
Sequence Bundles retain sequence identity
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pLogo
Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
M Kultys, L Nicholas, R Schwarz, N Goldman, J King, BMC Proceedings 2014, 8 (Suppl 2): S8
Sequence bundles for effective sequence comparison
Comparison to pLogo
Sequence Bundles
pLogo
calmodulin-dependent protein kinase II (CaMKII)
Information extraction from MSAs
• Dimension reduction
• Association between sequences and sites
• Explorative analysis
Correspondence Analysis
Correspondence Analysis on Multiple Alignments
Fisher scores as a numerical embedding
Detecting species-site dependencies in large multiple sequence alignments.
Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Müller-Reible C, Dandekar T, Karchin R, Schultz J, Müller T.,
Nucleic Acids Res. 2009 Oct;37(18)
Neisseria surface antigen fHBP
Neisseria surface antigen fHBP
Correspondence Analysis
ALVIS – integrating visualisation and analysis
• Fully interactive
• Sequence
Bundles
visualisation
• Tree inference
and visualisation
• Correspondence
Analysis
Customisable rendering engine
http://www.bitbucket.org/rfs/alvis
ALVIS – alphabet orderings
• full coverage of > 200 AAindex amino acid indices
• custom alphabets supported
ALVIS – positioning options
absolute positioning
relative positioning
ALVIS – HAD phosphatases
ALVIS – HAD phosphatases
More from
UniProt Feature Viewer
• View all protein
features in one
place
• Zoom & drag
view
• Variant viewer
• BioJS (use in
your own
resource)
• Coming to
www.uniprot.org
early 2016
BioLayout Express 3D (http://www.biolayout.org)
Skylign (http://skylign.org)
Clanviewer / Pfam
Acknowledgements
EBI:
Nick Goldman
Asif Tamuri
Science Practice:
Marek Kultys
James King
James Godwin
Ana Florescu
Science
Practice