SUMMARY: The Unipept Visualizations library is a JavaScript package to generate interactive visualizations of both hierarchical and non-hierarchical quantitative data. It provides four different visualizations: a sunburst, a treemap, a treeview and a heatmap. Every visualization is fully configurable, supports TypeScript and uses the excellent D3.js library. AVAILABILITY AND IMPLEMENTATION: The Unipept Visualizations library is available for download on NPM: https://npmjs.com/unipept-visualizations. All source code is freely available from GitHub under the MIT license: https://github.com/unipept/unipept-visualizations.

Motivation: Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. Results: We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Availability and Implementation: Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . Contact: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.

Comparing the top k elements between two or more ranked results is a common task in many contexts and settings. A few measures have been proposed to compare top k lists with attractive mathematical properties, but they face a number of pitfalls and shortcomings in practice. This work introduces a new measure to compare any two top k lists based on measuring the information these lists convey. Our method investigates the compressibility of the lists, and the length of the message to encode losslessly the lists gives a natural and robust measure of their variability. This information-theoretic measure objectively reconciles all the main considerations that arise when measuring (dis-)similarity between lists: the extent of their non-overlapping elements, the amount of disarray among overlapping elements, the measurement of displacement of actual ranks (positions) of their overlapping elements. We demonstrate that our measure is intuitively simple and superior to other commonly used measures. To the best of our knowledge, this is the first attempt to address the problem using information compression as its basis.

MOTIVATION: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. RESULTS: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. AVAILABILITY: http://lcb.infotech.monash.edu.au/I-value. SUPPLEMENTARY INFORMATION: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html.