A computation tool for the estimation of biomass composition from genomic and transcriptomic information

Abstract

Given the huge potential impact of the growing number of complete genome-scale metabolic network reconstructions of organisms, it is necessary to use bioinformatics tools to simplify and accelerate the course of knowledge in this field. One essential component of genome-scale metabolic model is biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information. In this work it is proposed a Java tool that estimates biomass composition in amino acids and nucleotides, from genome and transcriptomic information, using as input files sequences in FASTA format and files with transcriptomic data in csv format. This application allows to obtain the results rapidly and is also a user-friendly tool since facilitates its use by users with any or little background in informatics.