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Registro Completo |
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Biblioteca(s): |
Embrapa Soja. |
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Data corrente: |
25/04/2018 |
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Data da última atualização: |
25/04/2018 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
LOPES, I. de O. N.; SCHLIEP, A.; CARVALHO, A. C. P. de L. F. de. |
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Afiliação: |
IVANI DE OLIVEIRA NEGRAO LOPES, CNPSO; ALEXANDER SCHLIEP; ANDRÉ C. P. de L. F de CARVALHO. |
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Título: |
The discriminant power of RNA features for pre-miRNA recognition. |
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Ano de publicação: |
2014 |
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Fonte/Imprenta: |
BMC Bioinformatics, London, v. 15, p.124, 2014. |
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ISSN: |
1471-2105 |
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Idioma: |
Inglês |
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Conteúdo: |
Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. In this work, we analyze the discriminant power of seven feature sets, which are used in six pre-miRNA prediction tools. The analysis is based on the classification performance achieved with these feature sets for the training algorithms used in these tools. We also evaluate feature discrimination through the F-score and feature importance in the induction of random forests. Small or non-significant differences were found among the estimated classification performances of classifiers induced using sets with diversification of features, despite the wide differences in their dimension. Inspired in these results, we obtained a lower-dimensional feature set, which achieved a sensitivity of 90% and a specificity of 95%. These estimates are within 0.1% of the maximal values obtained with any feature set (SELECT, Section? Results and discussion?) while it is 34 times faster to compute. Even compared to another feature set (FS2, see Section? Results and discussion?), which is the computationally least expensive feature set of those from the literature which perform within 0.1% of the maximal values, it is 34 times faster to compute. The results obtained by the tools used as references in the experiments carried out showed that five out of these six tools have lower sensitivity or specificity. In miRNA discovery the number of putative miRNA loci is in the order of millions. Analysis of putative pre-miRNAs using a computationally expensive feature set would be wasteful or even unfeasible for large genomes. In this work, we propose a relatively inexpensive feature set and explore most of the learning aspects implemented in current ab-initio pre-miRNA prediction tools, which may lead to the development of efficient ab-initio pre-miRNA discovery tools. The material to reproduce the main results from this paper can be downloaded from http://bioinformatics.rutgers. edu/Static/Software/discriminant.tar.gz MenosComputational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. In this work, we analyze the discriminant power of seven feature sets, which are used in six pre-miRNA prediction tools. The analysis is based on the classification performance achieved with these feature sets for the training algorithms used in these tools. We also evaluate feature discrimination through the F-score and feature importance in the induction of random forests. Small or non-significant differences were found among the estimated classification performances of classifiers induced using sets with diversification of features, despite the wide differences in their dimension. Inspired in these results, we obtained a lower-dimensional feature set, which achieved a sensitivity of 90% and a specificity of 95%. These estimates are within 0.1% of the maximal values obtained with any feature set (SELECT, Section? Results and discussion?) while it is 34 times faster to compute. Even compared to another feature set (FS2, see Section? Results and discussion?), which is the computationally least expensive feature set of those from the literature which perform within 0.1% of the maximal values, it is 34 times faster to compute. The results obtained by the tools used as references in the experiments c... Mostrar Tudo |
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Palavras-Chave: |
Bioinformática. |
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Categoria do assunto: |
-- |
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Marc: |
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100 1 $aLOPES, I. de O. N.
245 $aThe discriminant power of RNA features for pre-miRNA recognition.$h[electronic resource]
260 $c2014
520 $aComputational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. In this work, we analyze the discriminant power of seven feature sets, which are used in six pre-miRNA prediction tools. The analysis is based on the classification performance achieved with these feature sets for the training algorithms used in these tools. We also evaluate feature discrimination through the F-score and feature importance in the induction of random forests. Small or non-significant differences were found among the estimated classification performances of classifiers induced using sets with diversification of features, despite the wide differences in their dimension. Inspired in these results, we obtained a lower-dimensional feature set, which achieved a sensitivity of 90% and a specificity of 95%. These estimates are within 0.1% of the maximal values obtained with any feature set (SELECT, Section? Results and discussion?) while it is 34 times faster to compute. Even compared to another feature set (FS2, see Section? Results and discussion?), which is the computationally least expensive feature set of those from the literature which perform within 0.1% of the maximal values, it is 34 times faster to compute. The results obtained by the tools used as references in the experiments carried out showed that five out of these six tools have lower sensitivity or specificity. In miRNA discovery the number of putative miRNA loci is in the order of millions. Analysis of putative pre-miRNAs using a computationally expensive feature set would be wasteful or even unfeasible for large genomes. In this work, we propose a relatively inexpensive feature set and explore most of the learning aspects implemented in current ab-initio pre-miRNA prediction tools, which may lead to the development of efficient ab-initio pre-miRNA discovery tools. The material to reproduce the main results from this paper can be downloaded from http://bioinformatics.rutgers. edu/Static/Software/discriminant.tar.gz
653 $aBioinformática
700 1 $aSCHLIEP, A.
700 1 $aCARVALHO, A. C. P. de L. F. de
773 $tBMC Bioinformatics, London$gv. 15, p.124, 2014.
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Registro original: |
Embrapa Soja (CNPSO) |
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| 5. |  | CARNEIRO, A. M.; CARVALHO, S. R. de; SOUTO, S. M.; CESAR, T. I. Competição entre variedades e híbridos de Sorghum vulgare. Influência de épocas, espaçamento e densidade de plantio na produção. Pesquisa Agropecuária Brasileira, Rio de Janeiro, v. 7, p. 47-51, 1972. (Zootecnia, 1). Título em inglês: Effect of seeding time row spacing, and plant density of yields of forage sorghums.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 8. | | CAMARGO FILHO, S. T.; CARVALHO, S. R.; PALMIERI, F.; ARONOVICH, S. Recovery of degraded agricultural land by introduction of fodder grasses and arboreous leguminous plants. Paty do Alferes County, RJ, Brazil. In: INTERNATIONAL CONFERENCE ON LAND DEGRADATION 3., AND MEETING OF THE IUSS SUBCOMISSION C - SOIL AND WATER CONSERVATION, 2001, Rio de Janeiro. Conference guide, program and book of abstracts... Rio de Janeiro: Embrapa; IUSS; IAC; SBCS, 2001. p.143| Biblioteca(s): Embrapa Solos. |
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| 9. | | CARVALHO, S. R. de; BRUAND, A.; HARDY, M.; LEPRUN, J.-C.; JAMAGNE, M. Tassement des sols ferrallitiques podzolico vermelho amarelo sous culture de canne à sucre (Etat de Rio de Janeiro, Brésil): apport d'une analyse de la porosité associée à une connaissance détaillée de la phase minérale. Cahiers ORSTOM. Série Pédologie, v. 26, n. 3, p. 195-212, 1991.| Tipo: Artigo em Periódico Indexado |
| Biblioteca(s): Embrapa Solos. |
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| 10. | | FARIA, P. F. L.; CARVALHO, E. M. R. de; LIMA, C. R.; CARVALHO, S. R. de. Uso da cama de frango e da silagem de milho na alimentação de novilhas leiteiras durante a estação seca. Pesquisa Agropecuária Brasileira, Brasília, DF, v. 10, n. 4, p. 37-41, 1975. (Zootecnia). Título em inglês: Corn silage and poultry litter for dairy heifers during the dry season.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 11. | | CARVALHO, S. R. de; SILVA, A. T. da S.; COSTA, F. A.; SOUTO, S. M.; LUCAS, E. D. de. Influência da irrigação e da adubação em dois cultivares de capim elefante (Pennisetum purpureum). Pesquisa Agropecuária Brasileira, Brasília, DF, v. 10, n. 4, p. 23-30, 1975. (Zootecnia). Título em inglês: Effects of irrigation and soil fertilization on two cultivars of elephantgrass (Pennisetum purpureum).| Biblioteca(s): Embrapa Unidades Centrais. |
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| 13. | | CARVALHO, S. R. de; DIAS, P. F.; CAMARGO FILHO, S. T.; BLANCANEAUX, P.; ARONOVICH, S.; FRANCO, A. R. Recuperacao de areas degradadas no Municipio de Paty do Alferes, pela introducao de gramineas forrageiras e leguminosas herbaceas e arboreas. In: WORKSHOP NACIONAL DE AGRICULTURA SUSTENTAVEL EM REGIOES DE RELEVO ACIDENTADO, 3., 1997. Paty do Alferes, RJ. Anais... Rio de Janeiro: EMBRAPA-CNPS, 1998. CD-ROM Nao paginado.| Biblioteca(s): Embrapa Solos. |
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| 14. | | BOTTECHIA, R. J.; FEIDEN, A.; ALMEIDA, D. L. de; AQUINO, A. M. de; LIGNON, G. B.; RIBEIRO, R. de L. D.; CARVALHO, S. R. de. Desempenho de animais em sistema de produção agroecológica. In: ENCONTRO DA SOCIEDADE BRASILEIRA DE SISTEMAS DE PRODUÇÃO, 3., 1998, Florianópolis. Anais [...]. Florianópolis: Sociedade Brasileira de Sistemas de Produção, 1998. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Solos. |
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| 17. | | ALMEIDA, D. L. de; GUERRA, J. G. M.; RIBEIRO, R. de L. D.; ABBOUD, A. C. de S.; CARVALHO, S. R. de; FEIDEN, A. Uma proposta de pesquisa em sistemas de produção: o sistema integrado de produção agroecológica "Fazendinha Agroecológica Km 47". In: ENCONTRO DA SOCIEDADE BRASILEIRA DE SISTEMAS DE PRODUÇÃO, 3., 1998, Florianópolis. Anais [...]. Florianópolis: Sociedade Brasileira de Sistemas de Produção, 1998. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Solos. |
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| 18. | | GOULART, F. F.; PERFECTO, I.; VANDERMEER, J.; BOUCHER, D.; CHAPPELL, M. J.; FERNANDES, G. W.; SCARIOT, A.; SILVA, M. C. da; OLIVEIRA, W.; NEVILLE, R.; MOORE, J.; BUSTAMANTE, M.; CARVALHO, S. R.; SOARES-FILHO, B. Emissions from cattle farming in Brazil. Nature Climate Change, v. 6, p. 893-894, 2016.| Tipo: Nota Técnica/Nota Científica |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 19. | | PEREIRA, R. G. de A.; TOWNSEND, C. R.; SALMAN, A. K. D.; LEONIDAS, F. das C.; CARVALHO, J. O. M. de; CARVALHO, S. R. de P.; JOBEL; PANIZI, E.; RIBEIRO, M. A. G.; SOUZA, J. P. de. Programa de desenvolvimento da ovinocultura para a agricultura familiar em Rondônia. In: SIMPÓSIO SOBRE INOVAÇÃO E CRIATIVIDADE CIENTÍFICA NA EMBRAPA, 2., 2010, Brasília, DF. Trabalhos apresentados e documentos... Brasília, DF: Embrapa-DPD, 2010. 1 p. 1 CD-ROM.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Rondônia. |
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| 20. | | PALMIERI, F.; LUMBRERAS, J. F.; CUNHA, T. J. F.; TOSTO, S. G.; MACEDO, J. R.; AMARAL, F. C. S.; CAPECHE, C. L.; CARVALHO JUNIOR, W.; MARTORANO, L. G.; GOMES, J. B. V.; CARVALHO, S. R.; ANJOS, L. H. C.; CEDDIA, M. B.; CAMARGO, S. T.; PEIXOTO, M. N. O.; MARQUES, J. S. An approach for sustainable land management in the montainous Atlantic biome, Paty do Alferes Couty, Rio de Janeiro, RJ, Brazil. In: INTERNATIONAL CONFERENCE ON LAND DEGRADATION, 3.; MEETING OF THE IUSS SUBCOMMISSION C - SOIL AND WATER CONSERVATION, 2001, Rio de Janeiro. Conference guide, program and book of abstracts... Rio de Janeiro: Embrapa: IUSS: IAC: SBCS, 2001. p. 113.| Biblioteca(s): Embrapa Solos. |
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| Registros recuperados : 21 | |
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