ArticleBMC proceedings2014
Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
Article in BMC proceedings, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- SARS-CoV-2 3CLpro whole human proteome cleavage prediction and enrichment/depletion analysis.Computational biology and chemistry · 2022Article
- Tasks, Techniques, and Tools for Genomic Data Visualization.Computer graphics forum : journal of the European Association for Computer Graphics · 2019Article
- MSAViewer: interactive JavaScript visualization of multiple sequence alignments.Bioinformatics (Oxford, England) · 2016Article
- ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.Nucleic acids research · 2016Article
- Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests.BMC proceedings · 2014Article
- ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.BMC proceedings · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe 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 methods (i.e. the Sequence Logo) by enabling Sequence Bundles to give salient visual expression to sequence motifs and other data features, which would otherwise remain hidden.
methodsFor the development of Sequence Bundles we employed research-led information design methodologies. Sequences are encoded as uninterrupted, semi-opaque lines plotted on a 2-dimensional reconfigurable grid. Each line represents a single sequence. The thickness and opacity of the stack at each residue in each position indicates the level of conservation and the lines' curved paths expose patterns in correlation and functionality. Several MSAs can be visualised in a composite image. The Sequence Bundles method is designed to favour a tangible, continuous and intuitive display of information.
resultsWe have developed a software demonstration application for generating a Sequence Bundles visualisation of MSAs provided for the BioVis 2013 redesign contest. A subsequent exploration of the visualised line patterns allowed for the discovery of a number of interesting features in the dataset. Reported features include the extreme conservation of sequences displaying a specific residue and bifurcations of the consensus sequence.
conclusionsSequence Bundles is a novel method for visualisation of MSAs and the discovery of sequence motifs. It can aid in generating new insight and hypothesis making. Sequence Bundles is well disposed for future implementation as an interactive visual analytics software, which can complement existing visualisation tools.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.