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Estimation of biomass composition from genomic and transcriptomic information

Santos, Sophia ; Rocha, Isabel

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genome-scale metabolic model is its 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, providing reliable data without the need of performing lab experiments. In this work a java tool is proposed that estimates microbial 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 the csv format. This application allows to obtain the results rapidly and is also a user-friendly tool for users with any or little background in informatics (http://darwin.di.uminho.pt/biomass/). The results obtained using this tool are fairly close to experimental data, showing that the estimation of amino acid and nucleotide compositions from genome information and from transcriptomic data is a good alternative when no experimental data is available.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Santos, Sophia ; Rocha, Isabel  (2016)  Estimation of biomass composition from genomic and transcriptomic information. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 13(2): Special Issue: Selected extended papers of the 10th International Conference on Practical Applications of Computational Biology and Bioinformatics, Seville, Spain, 2016. Guest editors: Mohd Saberi Mohamad, Miguel P. Rocha, Florentino Fdez-Riverola, Francisco J. Domínguez Mayo, Juan F. De Paz, 2016

Online-Journal: http://journal.imbio.de/article.php?aid=285
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2017/5440



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