Proceedings of the 3rd Annual Symposium on Biological Data Visualization: Data Analysis and Redesign Contests

Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests

In 2011, the BioVis symposium of the IEEE VisWeek conferences inaugurated a new variety of data analysis contest. Aimed at fostering collaborations between computational scientists and biologists, the BioVis c...

Authors: William C Ray, R Wolfgang Rumpf, Brandon Sullivan, Nicholas Callahan, Thomas Magliery, Raghu Machiraju, Bang Wong, Martin Krzywinski and Christopher W Bartlett

Integrative visual analysis of protein sequence mutations

An important aspect of studying the relationship between protein sequence, structure and function is the molecular characterization of the effect of protein mutations. To understand the functional impact of am...

Authors: Nadezhda T Doncheva, Karsten Klein, John H Morris, Michael Wybrow, Francisco S Domingues and Mario Albrecht

FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families

Knowledge of the 3D structure and functionality of proteins can lead to insight into the associated cellular processes, speed up the creation of pharmaceutical products, and develop drugs that are more effecti...

Authors: Timothy Luciani, John Wenskovitch, Koonwah Chen, David Koes, Timothy Travers and G Elisabeta Marai

VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation

In this paper, we propose an interactive visualization called VERMONT which tackles the problem of visualizing mutations and infers their possible effects on the conservation of physicochemical and topological...

Authors: Sabrina A Silveira, Alexandre V Fassio, Valdete M Gonçalves-Almeida, Elisa B de Lima, Yussif T Barcelos, Flávia F Aburjaile, Laerte M Rodrigues, Wagner Meira Jr and Raquel C de Melo-Minardi

Mu-8: visualizing differences between proteins and their families

A complete understanding of the relationship between the amino acid sequence and resulting protein function remains an open problem in the biophysical sciences. Current approaches often rely on diagnosing func...

Authors: Johnathan D Mercer, Balaji Pandian, Alexander Lex, Nicolas Bonneel and Hanspeter Pfister

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visuali...

Authors: Alberto I Roca

Seeing the results of a mutation with a vertex weighted hierarchical graph

We represent the protein structure of scTIM with a graph-theoretic model. We construct a hierarchical graph with three layers - a top level, a midlevel and a bottom level. The top level graph is a representati...

Authors: Debra J Knisley and Jeff R Knisley

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs

We introduce Sequence Bundles--a novel data visualisation method for representing multiple sequence alignments (MSAs). We identify and address key limitations of the existing bioinformatics data visualisation ...

Authors: Marek Kultys, Lydia Nicholas, Roland Schwarz, Nick Goldman and James King

Sequence Diversity Diagram for comparative analysis of multiple sequence alignments

The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences. Although it effectively communicates the amount of inf...

Authors: Ryo Sakai and Jan Aerts

Erratum to: Sequence Diversity Diagram for comparative analysis of multiple sequence alignments

Authors: Ryo Sakai and Jan Aerts