RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins

Abstract

Summary: Patterns of mutational correlations, learnt from protein sequences, have been shown to be informative of co-evolutionary sectors that are tightly linked to functional and/or structural properties of proteins. Previously, we developed a statistical inference method, robust co-evolutionary analysis (RoCA), to reliably predict co-evolutionary sectors of proteins, while controlling for statistical errors caused by limited data. RoCA was demonstrated on multiple viral proteins, with the inferred sectors showing close correspondences with experimentally-known biochemical domains. To facilitate seamless use of RoCA and promote more widespread application to protein data, here we present a standalone cross-platform package 'RocaSec' which features an easy-to-use GUI. The package only requires the multiple sequence alignment of a protein for inferring the co-evolutionary sectors. In addition, when information on the protein biochemical domains is provided, RocaSec returns the corresponding statistical association between the inferred sectors and biochemical domains.

Availability and implementation: The RocaSec software is publicly available under the MIT License at https://github.com/ahmedaq/RocaSec.

Supplementary information: Supplementary data are available at Bioinformatics online.