Um sistema para análise de genomas a partir de metagenomas
Abstract
This paper presents a system developed to analyze genomes data which is part of metagenomes sequencing. As a result, some tools were developed to identify the species of metagenomics sequences, for helping the assembly process and to analyze the taxonomy of the assembled sequences in order to identify the similarity between microorganisms' genomes in metagenome.
Keywords:
a
References
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Digiampietri, L. A., Pereira, V. M., Costa, C. I., dos Santos-Junior, G. J., Stefanini, F. M., e Santiago, C. R. (2014). An extensible framework for genomic and metagenomic analysis. In Advances in Bioinformatics and Computational Biology, volume 8826 of Lecture Notes in Computer Science, pages 1–8. Springer.
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Liu, B., Gibbons, T., e Pop, M. G. M. (2010). Metaphyler: Taxonomic profiling for metagenomic sequences. In International Conference on Bioinformatics and Biomedicine (BIBM), pages 95–100.
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Martins, L. F., Antunes, L. P., Pascon, R. C., de Oliveira, J. C. F., Digiampietri, L. A., Barbosa, D., Peixoto, B. M., Vallim, M. A., Viana-Niero, C., Ostroski, E. H., Telles, G. P., Dias, Z., da Cruz, J. B., Juliano, L., Verjovski-Almeida, S., da Silva, A. M., e Setubal, J. C. (2013). Metagenomic analysis of a tropical composting operation at the sã o paulo zoo park reveals diversity of biomass degradation functions and organisms. Plos One, 8:1–13.
Meyer, F., Paarmann, D., D’Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., Wilkening, J., e Edwards, R. A. (2008). The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9(1):386.
Setubal, J. C. e Meidanis, J. (1997). Introduction to Computational Molecular Biology. PWS Publishing Company, Boston, EUA.
Sharon, I. e Banfield, J. F. (2013). Genomes from metagenomics. Science, 342:1057–1058.
Davenport, C. F., Neugebauer, J., Beckmann, N., Friedrich, B., Kameri, B., Kokott, S., Paetow, M., Siekmann, B., Wieding-Drewes, M., Wienh¨ofer, M., Wolf, S., T¨ummler, B., Ahlers, V., e Sprengel, F. (2012). Genometa - a fast and accurate classifier for short metagenomic shotgun reads. PLOS ONE, 7(8):e41224.
Digiampietri, L. A., Pereira, V. M., Costa, C. I., dos Santos-Junior, G. J., Stefanini, F. M., e Santiago, C. R. (2014). An extensible framework for genomic and metagenomic analysis. In Advances in Bioinformatics and Computational Biology, volume 8826 of Lecture Notes in Computer Science, pages 1–8. Springer.
Gerlach, W. e Stoye, J. (2011). Taxonomic classification of metagenomic shotgun sequences with carma3. Nucleid Acids Research, 39(14).
Haque, M. M., Ghosh, T. S., Komanduri, D., e Mande, S. S. (2009). Sort-items: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics, 25(14):1722–1730.
Huson, D. H., Auch, A. F., Qi, J., e C., S. S. (2007). Megan analysis of metagenomic data. Genome Research, 17(3):377–386.
Liu, B., Gibbons, T., e Pop, M. G. M. (2010). Metaphyler: Taxonomic profiling for metagenomic sequences. In International Conference on Bioinformatics and Biomedicine (BIBM), pages 95–100.
Luscombe, N. M., Greenbaum, D., e Gerstein, M. (2001). What is bioinformatics? A proposed definition and overview of the field. Methods of information in medicine, 40(4):346–358.
Martins, L. F., Antunes, L. P., Pascon, R. C., de Oliveira, J. C. F., Digiampietri, L. A., Barbosa, D., Peixoto, B. M., Vallim, M. A., Viana-Niero, C., Ostroski, E. H., Telles, G. P., Dias, Z., da Cruz, J. B., Juliano, L., Verjovski-Almeida, S., da Silva, A. M., e Setubal, J. C. (2013). Metagenomic analysis of a tropical composting operation at the sã o paulo zoo park reveals diversity of biomass degradation functions and organisms. Plos One, 8:1–13.
Meyer, F., Paarmann, D., D’Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., Wilkening, J., e Edwards, R. A. (2008). The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9(1):386.
Setubal, J. C. e Meidanis, J. (1997). Introduction to Computational Molecular Biology. PWS Publishing Company, Boston, EUA.
Sharon, I. e Banfield, J. F. (2013). Genomes from metagenomics. Science, 342:1057–1058.
Published
2015-08-26
How to Cite
PEREIRA, Vivian; DOS SANTOS JÚNIOR, Geraldo; DIGIAMPIETRI, Luciano.
Um sistema para análise de genomas a partir de metagenomas. In: BRAZILIAN E-SCIENCE WORKSHOP (BRESCI), 9. , 2015, Recife.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2015
.
p. 1-10.
ISSN 2763-8774.
DOI: https://doi.org/10.5753/bresci.2015.7201.
