ProdMX: Rapid query and analysis of protein functional domain based on compressed sparse matrices

By November 24, 2020Publications

Visanu Wanchai, Intawat Nookaew, and David W. Ussery

Computational and structural biotechnology journal. 2020 Nov 24.

Abstract

Large-scale protein analysis has been used to characterize large numbers of proteins across numerous species. One of the applications is to use as a high-throughput screening method for pathogenicity of genomes. Unlike sequence homology methods, protein comparison at a functional level provides us with a unique opportunity to classify proteins, based on their functional structures without dealing with sequence complexity of distantly related species. Protein functions can be abstractly described by a set of protein functional domains, such as PfamA domains; a set of genomes can then be mapped to a matrix, with each row representing a genome, and the columns representing the presence or absence of a given functional domain. However, a powerful tool is needed to analyze the large sparse matrices generated by millions of genomes that will become available in the near future. The ProdMX is a tool with user-friendly utilities developed to facilitate high-throughput analysis of proteins with an ability to be included as an effective module in the high-throughput pipeline. The ProdMX employs a compressed sparse matrix algorithm to reduce computational resources and time used to perform the matrix manipulation during functional domain analysis. The ProdMX is a free and publicly available Python package which can be installed with popular package mangers such as PyPI and Conda, or with a standard installer from source code available on the ProdMX GitHub repository at https://github.com/visanuwan/prodmx.

Keywords Proteins; Protein functional domain; Domain architecture; Comparative genomics; Python; Compressed sparse matrix

Read the publication here: https://www.sciencedirect.com/science/article/pii/S2001037020304451

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