Abstract
The structure, dynamics and, ultimately, biological function of proteins and nucleic acids are determined by the physicochemical properties of their primary sequences. Such properties are frequently captured via one-dimensional profile plots depicting a given physicochemical variable as a function of sequence position. Hydrophobicity, charge or structural disorder in proteins or nucleobase-density in nucleic acids are routinely visualized in this manner to analyze sequences at a glance. Such visualizations, however, are typically created case-by-case in a purely static manner, employ fixed visualization parameters only and do not enable a quantitative comparison between different sequences. Here, we present VOLPES (volpes.univie.ac.at), a user-friendly web server and the corresponding JavaScript library that enable a fully interactive, multifunctional visualization, analysis and comparison of the physicochemical properties of protein and nucleic-acid sequences, allowing unprecedented insight into biological sequence data and creating a starting point for further in-depth exploration.
Highlights
The structure, dynamics and, biological function of proteins and nucleic acids are determined by the physicochemical properties of their primary sequences
A foundational principle of bioinformatics is that biological function is encoded in and can be related to the primary sequences of nucleic acids and proteins
Over 600 different physicochemical property scales of amino acids and nucleobases are available in VOLPES, with detailed descriptions for each scale, allowing the user to quickly browse through
Summary
A foundational principle of bioinformatics is that biological function is encoded in and can be related to the primary sequences of nucleic acids and proteins. Hydrophobicity profiles are often employed to learn about the structural features and domain boundaries in proteins Such profiles are routinely used to ascertain the location of transmembrane regions in membrane proteins [1,2,3,4]. Tools featuring more advanced features are not available as web servers but rather as downloadable standalone packages [3,20] In response to these challenges, we present here VOLPES, a multifunctional web server and a JavaScript library for highly customizable, interactive visualization, analysis and comparison of the physicochemical properties of protein and RNA sequences. Nucleic Acids Research, 2019, Vol 47, Web Server issue W633 dard methods of primary sequence analysis and comparison
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