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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://www.alice.cnptia.embrapa.br/alice/bitstream/doc/1045860/1/AutomaticlearningofpremiRNAsfromdifferentspecies.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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Registro Completo
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Biblioteca(s): |
Embrapa Pantanal. |
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Data corrente: |
13/12/2010 |
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Data da última atualização: |
14/12/2010 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
COSTA, R. M. R. DA.; SILVA, S. E. DA.; MATEUS, L. A. DE F.; CATELLA, A. C. |
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Afiliação: |
ROSA MARIA RODRIGUES DA COSTA, UFMT; SAMUEL ELIAS DA SILVA, UFMT; LÚCIA APARECIDA DE FÁTIMA MATEUS, UFMT; AGOSTINHO CARLOS CATELLA, CPAP. |
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Título: |
Censo estrutural da pesca na Bacia do Alto Paraguai estado de Mato Grosso. |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
SIMPÓSIO SOBRE RECURSOS NATURAIS E SOCIOECONÔMICOS DO PANTANAL, 5., 2010, Corumbá, MS. Anais... Corumbá: Embrapa Pantanal: UFMS; Campinas: ICS do Brasil, 2010. 1 CD-ROM SIMPAN 2010. |
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Páginas: |
Não Paginado |
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Idioma: |
Português |
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Palavras-Chave: |
Bacia do Alto Paraguai. |
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Thesagro: |
Censo; Pesca. |
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Categoria do assunto: |
-- |
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URL: |
https://www.alice.cnptia.embrapa.br/alice/bitstream/doc/869528/1/013R.pdf
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Marc: |
LEADER 00670nam a2200181 a 4500
001 1869528
005 2010-12-14
008 2010 bl uuuu u00u1 u #d
100 1 $aCOSTA, R. M. R. DA.
245 $aCenso estrutural da pesca na Bacia do Alto Paraguai estado de Mato Grosso.
260 $aSIMPÓSIO SOBRE RECURSOS NATURAIS E SOCIOECONÔMICOS DO PANTANAL, 5., 2010, Corumbá, MS. Anais... Corumbá: Embrapa Pantanal: UFMS; Campinas: ICS do Brasil, 2010. 1 CD-ROM SIMPAN 2010.$c2010
300 $aNão Paginado
650 $aCenso
650 $aPesca
653 $aBacia do Alto Paraguai
700 1 $aSILVA, S. E. DA.
700 1 $aMATEUS, L. A. DE F.
700 1 $aCATELLA, A. C.
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Embrapa Pantanal (CPAP) |
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