Sequence Bundles

Sequence Bundles is a novel method for visualising biological data and discovering sequence motifs that would otherwise remain hidden.

We designed Sequence Bundles at Science Practice. I initiated, managed, and directed the project, set up a collaboration with the Goldman group at the European Bioinformatics Institute, secured funding from Innovate UK, and co-authored academic articles, including our latest publication in Nucleic Acids Research (2016).

Sequence Bundles visualisation
Sequence Bundles visualisation

Sequence Bundles are designed to help bioinformaticians discover and explore sequence motifs in protein and DNA Multiple Sequence Alignments (MSAs).

The Sequence Bundles method is a cousin of parallel coordinates. The X-axis shows all sequence positions (here 36). The Y-axis lists all possible residues in the sequence (here 20 amino acids + gap). Each sequence is represented with a line. Lines are continuous and semi-transparent, so it is easy to see as they converge in regions of consensus, and as they diverge in areas of variability.

Sequence Bundles have been implemented in two software tools.

At Science Practice we developed an online visualisation tool. It provides a quick and easy way to visualise users' own protein data. Images generated with our online tool can be used in publications too.

Screen from the Sequence Bundles web-app

We also collaborated with the Goldman group at EMBL-EBI to implement Sequence Bundles as the main visualisation tool in Alvis — an open-source desktop platform for visualisation, exploration, and analysis of MSAs. We introduced Alvis in our recent paper in Nucleic Acids Research (2016).

We worked on Sequence Bundles for almost 2.5 years. The project started with some quick sketches, interviews with experts, and a lot of research into visualisation in bioinformatics. We went through several rounds of design iteration: from concept drawings, to design mock-ups, to proof-of-concept prototypes. The project concluded in building actual bioinformatics software tools.

I outlined our design journey in a post on Science Practice blog.

Sketching to understand sequence logos Prof of concept prototype of Sequence Bundles in Processing

Sequence Bundles were published in:

Sequence Bundles in competitions:

  • Short-listed for the 2016 Kantar Information is Beautiful Award,
  • 2nd prize (tied) in the BioVis 2013 redesign contest.

I discussed Sequence Bundles at:

  • 3rd International Scientific conference on Information Design in Kraków, 2015,
  • Cambridge Visualization of Biological Information meetup in Cambridge, 2015,
  • Bioinformatics London meetup, 2015,
  • Think(in) Visual Communication international conference in Warsaw, 2014,
  • IDA 2014 Information Design Association conference in London,
  • 3rd IEEE symposium on Biological Data Visualisation BioVis 2013 in Atlanta.

Sequence Bundles were also shown at:

  • Art of Networks exhibition at the NetSciX conference in Wrocław in 2016,
  • Art of Networks II exhibition in New York Hall of Science in 2015.