Um sistema para análise de genomas a partir de metagenomas
Resumo
Este artigo apresenta um sistema desenvolvido com o objetivo de analisar dados dos genomas que fazem parte de sequenciamentos de metagenomas. Como resultado, foram desenvolvidas ferramentas para realizar a identificação das espécies presentes em sequências metagenômicas, auxiliar o processo de similaridade entre os genomas dos microorganismos presentes no metagenoma.
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Referências
Arumugam, M., Harrington, E. D., Foerstner, K. U., Raes, J., e Bork, P. (2010). Smashcommunity: a metagenomic annotation and analysis tool. Bioinformatics, 26(23):2977–2978.
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.
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.
Publicado
26/08/2015
Como Citar
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.
