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

Ahmed A. Quadeer, David Morales-Jimenez, Matthew R. McKay

Research output: Contribution to journalArticle

Abstract

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.
Original languageEnglish
Pages (from-to)2262-2263
Number of pages2
JournalBioinformatics
Volume36
Issue number7
Early online date04 Dec 2019
DOIs
Publication statusPublished - 01 Apr 2020

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