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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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Registro original: |
Embrapa Soja (CNPSO) |
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| 3. |  | GUERRA, M. P.; DAL VESCO, L. L.; PESCADOR, R.; SCHUELTER, A. R.; NODARI, R. O. Estabelecimento de um protocolo regenerativo para a micropropagação do abacaxizeiro. Pesquisa Agropecuária Brasileira, Brasília, DF, v. 34, n. 9, p.1557-63, set. 1999 Título em inglês: Establishment of a regenerative protocol for the pineapple micropropagation.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 4. | | GIRARDI, C. G.; RUTHNER, R. R.; GALVÃO, F.; CURCIO, G. R.; UHLMANN, A.; STÜRMER, S. L.; ZIMMER, E.; PESCADOR, R. Biomassa de espécies nativas em área sob processo de recuperação induzida na Bacia do Vale do Itajaí. In: CONGRESSO LATINO AMERICANO DE ECOLOGIA, 3.; CONGRESSO DE ECOLOGIA DO BRASIL, 9., 2009, São Lourenço. Ecologia e o futuro da biosfera. Anais. São Paulo: SEB, 2009.| Tipo: Artigo em Anais de Congresso |
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| 5. | | MÜLLER, M.; PESCADOR, R.; UHLMANN, A.; STURMER, S. L.; ZIMMER, E.; SEVEGNANI, L.; GIRARDI, C. G.; POZZOBON, M. Deposição de serapilheira e nutrientes minerais em área de revegetação induzida na planície do Rio Itajaí - Açu, SC, Brasil. In: CONGRESSO BRASILEIRO DE FISIOLOGIA VEGETAL, 13.; REUNIÃO LATINO-AMERICANA DE FISIOLOGIA VEGETAL MUDANÇAS CLIMÁTICAS E GLOBAIS: DO GENE À PLANTA, 14., 2011, Búzios, RJ. Livro de resumos... Campos dos Goytacazes: UENF, 2011. p. 145. Resumo OT026. Trabalhos publicados em Brazilian Journal of Plant Phisiology.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Florestas. |
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| 6. | | BRUNETTO, G.; AMBROSINI, V. G.; ROSA, D. J.; BORGHEZAN, M.; PESCADOR, R.; MELO, G. W. B. de; SOARES, C. R. F. S. S.; COMIN, J. J. Calcário como amenizante da toxidez de cobre em aveia preta (Avena strigosa) cultivada em solo de vinhedo: estado nutricional e parâmetros fisiológicos. In:CONGRESSO LATINO-AMERICANO DE VITICULTURA E ENOLOGIA, 15., 2015, Bento Gonçalves, RS. p. 070. XV Congresso Latino-Americano de Viticultura e Enologia E XIII Congresso Brasileiro de Viticultura e Enologia. Bento Gonçalves-RS, 3 a 7 de Novembro de 2015.| Tipo: Resumo em Anais de Congresso |
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| 7. | | POLESI, L. G.; FRAGA, H. P. F. de; VIEIRA, L. do N.; HERINGER, A. S.; ORNELLAS, T. S.; SANTOS, H. P. dos; GUERRA, M. P.; PESCADOR, R. Chloroplast ultrastructure and hormone endogenous levels are differently affected under light and dark conditions during in vitro culture of Guadua chacoensis (Rojas) Londoño & P. M. Peterson. Acta Physiologiae Plantarum , v. 41, n. 10, p. 1-12, Jan. 2019.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Uva e Vinho. |
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| 8. | | BENEDET, L.; COMIN, J. J.; PESCADOR, R.; OLIVEIRA, P. A. V. de; BELLI FILHO, P.; DE CONTI, L.; COUTO, R. da R.; LOVATO, P. E.; CESCO, S.; MIMMO, T.; BRUNETTO, G. Physiological changes in maize grown in soil with copper and zinc accumulation resulting from the addition of pig slurry and deep litter over 10 years. Water, Air and Soil Pollution, v. 227, n. 401, 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Suínos e Aves. |
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