MetQy-an R package to query metabolic functions of genes and genomes.

Andrea S Martinez-Vernon,Orkun S Soyer,Frederick Farrell,John Hancock

doi:10.1093/bioinformatics/bty447

Abstract

SummaryWith the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions. To this end, we developed MetQy, an open–source R package designed for query–based analysis of functional units in [meta]genomes and/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, MetQy contains visualization and analysis tools and facilitates KEGG’s flat file manipulation. Thus, MetQy enables better understanding of metabolic capabilities of known genomes or user–specified [meta]genomes by using the available information and can help guide studies in microbial ecology, metabolic engineering and synthetic biology.Availability and implementationThe MetQy R package is freely available and can be downloaded from our group’s website (http://osslab.lifesci.warwick.ac.uk) or GitHub (https://github.com/OSS-Lab/MetQy).

Highlights

The advent of molecular biology has made the characterisation and analysis of genomic sequences a key part of all areas of life sciences research
Summary: With the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions
We developed MetQy, an open–source R package designed for query–based analysis of functional units in [meta]genomes and/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG)

Summary

Introduction

The advent of molecular biology has made the characterisation and analysis of genomic sequences a key part of all areas of life sciences research. Its primary aim has been the digitising of current knowledge on genes and molecules and their interactions (Kanehisa, 1997; Kanehisa and Goto, 2000) and it includes 16 databases and 3 sequence data collections (Kanehisa et al, 2017). While these data can be analysed via different tools on the KEGG website, the existing web interface allows only specific retrieval of information and analyses. The MetQy package and GitHub wiki contain extensive documentation and usage examples for each function

Metabolic query functions

Parsing KEGG databases

Analysis and visualisation

Uses and applications