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Registro Completo |
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Biblioteca(s): |
Embrapa Soja. |
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Data corrente: |
30/05/2016 |
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Data da última atualização: |
26/07/2017 |
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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. P. de L. F. de. |
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Afiliação: |
IVANI DE OLIVEIRA NEGRAO LOPES, CNPSO; ALEXANDER SCHLIEP, Rutgers University, USA; ANDRÉ P. DE L. F. de CARVALHO, Instituto de Ciências Matemáticas e de Computação, São Carlos. |
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Título: |
Automatic learning of pre-miRNAs from different species. |
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Ano de publicação: |
2016 |
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Fonte/Imprenta: |
BMC Bioinformatics, v. 17, n. 224, 18 p., 2016. |
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ISSN: |
1471-2105 |
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DOI: |
10.1186/s12859-016-1036-3 |
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Idioma: |
Português |
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Conteúdo: |
Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower. While these biases are intrinsic to the species, their characterization can lead to computational approaches capable of diminishing their negative effect on the accuracy of pre-miRNAs predictive models. We investigate in this study how 45 predictive models induced for data sets from 45 species, distributed in eight subphyla/classes, perform when applied to a species different from the species used in its induction. Results: Our computational experiments show that the separability of pre-miRNAs and pseudo pre-miRNAs instances is species-dependent and no feature set performs well for all species, even within the same subphylum/class. Mitigating this species dependency, we show that an ensemble of classifiers reduced the classification errors for all 45 species. As the ensemble members were obtained using meaningful, and yet computationally viable feature sets, the ensembles also have a lower computational cost than individual classifiers that rely on energy stability parameters, which are of prohibitive computational cost in large scale applications. Conclusion: In this study, the combination of multiple pre-miRNAs feature sets and multiple learning biases enhanced the predictive accuracy of pre-miRNAs classifiers of 45 species. This is certainly a promising approach to be incorporated in miRNA discovery tools towards more accurate and less species-dependent tools. MenosDiscovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower. While these biases are intrinsic to the species, their characterization can lead to computational approaches capable of diminishing their negative effect on the accuracy of pre-miRNAs predictive models. We investigate in this study how 45 predictive models induced for data sets from 45 species, distributed in eight subphyla/classes, perform when applied to a species different from the species used in its induction. Results: Our computational experiments show that the separability of pre-miRNAs and pseudo pre-miRNAs instances is species-dependent and no feature set performs well for all species, even within the same subphylum/class. Mitigating this species dependency, we show that an ensemble of classifiers reduced the classification errors for all 45 species. As the ensemble members were obtained using meaningful, and yet computationally viable feature sets, the ensembles also have a lower computational cost than individual classifiers ... Mostrar Tudo |
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Palavras-Chave: |
Bioinformática. |
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Thesagro: |
Automação; Biologia. |
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Thesaurus Nal: |
Bioinformatics; Biological Sciences. |
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Categoria do assunto: |
S Ciências Biológicas |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/143864/1/Automatic-learning-of-pre-miRNAs-from-different-species.pdf
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Marc: |
LEADER 02586naa a2200229 a 4500
001 2045860
005 2017-07-26
008 2016 bl uuuu u00u1 u #d
022 $a1471-2105
024 7 $a10.1186/s12859-016-1036-3$2DOI
100 1 $aLOPES, I. de O. N.
245 $aAutomatic learning of pre-miRNAs from different species.$h[electronic resource]
260 $c2016
520 $aDiscovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower. While these biases are intrinsic to the species, their characterization can lead to computational approaches capable of diminishing their negative effect on the accuracy of pre-miRNAs predictive models. We investigate in this study how 45 predictive models induced for data sets from 45 species, distributed in eight subphyla/classes, perform when applied to a species different from the species used in its induction. Results: Our computational experiments show that the separability of pre-miRNAs and pseudo pre-miRNAs instances is species-dependent and no feature set performs well for all species, even within the same subphylum/class. Mitigating this species dependency, we show that an ensemble of classifiers reduced the classification errors for all 45 species. As the ensemble members were obtained using meaningful, and yet computationally viable feature sets, the ensembles also have a lower computational cost than individual classifiers that rely on energy stability parameters, which are of prohibitive computational cost in large scale applications. Conclusion: In this study, the combination of multiple pre-miRNAs feature sets and multiple learning biases enhanced the predictive accuracy of pre-miRNAs classifiers of 45 species. This is certainly a promising approach to be incorporated in miRNA discovery tools towards more accurate and less species-dependent tools.
650 $aBioinformatics
650 $aBiological Sciences
650 $aAutomação
650 $aBiologia
653 $aBioinformática
700 1 $aSCHLIEP, A.
700 1 $aCARVALHO, A. P. de L. F. de
773 $tBMC Bioinformatics$gv. 17, n. 224, 18 p., 2016.
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Registro original: |
Embrapa Soja (CNPSO) |
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| 5. |  | CAMARGO, M. N.; JACOMINE, P. K. T.; CARVALHO, A. P. de; LARACH, J. O. I. The Brazilian classification of latosols. In: INTERNATIONAL SOIL CLASSIFICATION WORKSHOP, 8., 1986, Rio de Janeiro. Classification, characterization and utilization of oxisols: proceedings. Rio de Janeiro: EMBRAPA-SNLCS: USDA-SMSS: University of Puerto Rico, 1988. pt. 1, p. 190-199.| Biblioteca(s): Embrapa Solos. |
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| 11. | | RESENDE, M. D. V. de; STURION, J. A.; CARVALHO, A. P. de; SIMEAO, R. M.; FERNANDES, J. S. C. Avaliacao genetica de populacoes, progenies, individuos e clones de erva-mate no Parana. In: CONGRESSO SUL-AMERICANO DA ERVA MATE, 2.; REUNIAO TECNICA DA ERVA MATE, 3., 2000, Encantado. Anais. Porto Alegre: Comissao dos Organizadores / Universidade do Rio Grande do Sul / Fundacao Estadual de Pesquisa Agropecuaria, 2000. p.57-59.| Biblioteca(s): Embrapa Florestas. |
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| 16. | | BOGNOLA, I. A.; POTTER, R. O.; CARVALHO, A. P. de; FASOLO, P. J.; BHERING, S. B.; MARTORANO, L. G. Caracterização dos solos do Município de Carambeí, PR. Rio de Janeiro: Embrapa Solos, 2002. 75 p. il. color. (Embrapa Solos. Boletim de pesquisa e desenvolvimento, 8). Acompanha 1 mapa, color. Escala 1:100.000. Mapa Levantamento Semidetalhado de Solos Município de Carambeí - Estado do Paraná.| Tipo: Boletim de Pesquisa e Desenvolvimento |
| Biblioteca(s): Embrapa Florestas; Embrapa Solos. |
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| 17. | | FASOLO, P. J.; CARVALHO, A. P. de; POTTER, R. O.; BOGNOLA, I. A.; BHERING, S. B.; MARTORANO, L. G. Caracterização dos solos do Município de Castro, PR. Rio de Janeiro: Embrapa Solos, 2002. 88 p. il. color. (Embrapa Solos. Boletim de pesquisa e desenvolvimento, 9). Acompanha 1 mapa, color. Escala 1:100.000. Mapa Levantamento Semidetalhado de Solos Município de Castro - Estado do Paraná.| Tipo: Boletim de Pesquisa e Desenvolvimento |
| Biblioteca(s): Embrapa Florestas; Embrapa Solos. |
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| Registros recuperados : 69 | |
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