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 | Acesso ao texto completo restrito à biblioteca da Embrapa Recursos Genéticos e Biotecnologia. Para informações adicionais entre em contato com cenargen.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
16/02/2012 |
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Data da última atualização: |
27/02/2023 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
VIEIRA, F. D.; PAIVA, S. R.; YAMAGISHI, M. E. B.; OLIVEIRA, S. R. de M.; HIGA, R. |
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Afiliação: |
FÁBIO DANILO VIEIRA, CNPTIA; SAMUEL REZENDE PAIVA, CENARGEN; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; STANLEY ROBSON DE MEDEIROS OLIVEIRA, CNPTIA; ROBERTO HIROSHI HIGA, CNPTIA. |
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Título: |
Databases & data integration text mining & information extraction. |
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Ano de publicação: |
2011 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional, 2011. |
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Páginas: |
Não paginado. |
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Idioma: |
Inglês |
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Notas: |
X-MEETING, 2011. |
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Conteúdo: |
In recent years, with the joint development of biotechnology and bioinformatics, applications that use DNA analysis in the animal breeding area have spread out. In particular, applications that make use of molecular markers of type SNP are among the most important ones. With the recent advances achieved by the DNA sequencing technology, it is possible to identify hundred of thousands of SNPs variants per animal. In this work, we propose a methodology to identify in a dataset a set of SNPs whose allele frequencies certify each of the sheep breeds (Creole, Santa Ines and Morada Nova). We used a dataset of SNP markers provided by the Sheep Genome Consortium International, obtained through the Network of Animal Genomics Embrapa. We applied data mining techniques, especially attribute selection methods and algorithms for generating association rules. The first step was to make the selection of attributes, due to the high number of SNP markers, with almost 60,000 markers for each animal. Subsequently, we applied the Apriori algorithm in order to generate association rules with the purpose of obtaining SNPs whose allelic values could determine the breed that each animal belongs to. The results showed that, with minimal support of 15% and minimum confidence of 90%, some SNPs have values that appear only in a particular breed. The best rules appear at the top of the list due to high values of support and confidence achieved. It was observed that the top 35 associations rules are related to Creole, with support of 30% and confidence of 100% . The first rule indicates that one of the selected markers with a certain a homozigous allele characterizes the breed is Creole, appearing in 22 records (30% of the total, which has 72 records) and 100% confidence, i.e., in 22 times that the marker came up with this value, the breed was related to Creole. The results need to be better evaluated and validated by experts, but they seem to be of great importance for future work. The methodology proposed in this work could be used to support breeding programs for sheep in progeny tests. References MACQUEEN, J. B. (1967). Some Methods for classification and Analysis of Multivariate Observations. MenosIn recent years, with the joint development of biotechnology and bioinformatics, applications that use DNA analysis in the animal breeding area have spread out. In particular, applications that make use of molecular markers of type SNP are among the most important ones. With the recent advances achieved by the DNA sequencing technology, it is possible to identify hundred of thousands of SNPs variants per animal. In this work, we propose a methodology to identify in a dataset a set of SNPs whose allele frequencies certify each of the sheep breeds (Creole, Santa Ines and Morada Nova). We used a dataset of SNP markers provided by the Sheep Genome Consortium International, obtained through the Network of Animal Genomics Embrapa. We applied data mining techniques, especially attribute selection methods and algorithms for generating association rules. The first step was to make the selection of attributes, due to the high number of SNP markers, with almost 60,000 markers for each animal. Subsequently, we applied the Apriori algorithm in order to generate association rules with the purpose of obtaining SNPs whose allelic values could determine the breed that each animal belongs to. The results showed that, with minimal support of 15% and minimum confidence of 90%, some SNPs have values that appear only in a particular breed. The best rules appear at the top of the list due to high values of support and confidence achieved. It was observed that the top 35 associations rules are rela... Mostrar Tudo |
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Palavras-Chave: |
Marcadores moleculares SNP; Mineração de texto; Recuperação da informação; Text mining. |
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Thesagro: |
Base de Dados. |
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Thesaurus Nal: |
Databases; Information retrieval. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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Marc: |
LEADER 03250nam a2200265 a 4500
001 1915906
005 2023-02-27
008 2011 bl uuuu u01u1 u #d
100 1 $aVIEIRA, F. D.
245 $aDatabases & data integration text mining & information extraction.$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional$c2011
300 $aNão paginado.
500 $aX-MEETING, 2011.
520 $aIn recent years, with the joint development of biotechnology and bioinformatics, applications that use DNA analysis in the animal breeding area have spread out. In particular, applications that make use of molecular markers of type SNP are among the most important ones. With the recent advances achieved by the DNA sequencing technology, it is possible to identify hundred of thousands of SNPs variants per animal. In this work, we propose a methodology to identify in a dataset a set of SNPs whose allele frequencies certify each of the sheep breeds (Creole, Santa Ines and Morada Nova). We used a dataset of SNP markers provided by the Sheep Genome Consortium International, obtained through the Network of Animal Genomics Embrapa. We applied data mining techniques, especially attribute selection methods and algorithms for generating association rules. The first step was to make the selection of attributes, due to the high number of SNP markers, with almost 60,000 markers for each animal. Subsequently, we applied the Apriori algorithm in order to generate association rules with the purpose of obtaining SNPs whose allelic values could determine the breed that each animal belongs to. The results showed that, with minimal support of 15% and minimum confidence of 90%, some SNPs have values that appear only in a particular breed. The best rules appear at the top of the list due to high values of support and confidence achieved. It was observed that the top 35 associations rules are related to Creole, with support of 30% and confidence of 100% . The first rule indicates that one of the selected markers with a certain a homozigous allele characterizes the breed is Creole, appearing in 22 records (30% of the total, which has 72 records) and 100% confidence, i.e., in 22 times that the marker came up with this value, the breed was related to Creole. The results need to be better evaluated and validated by experts, but they seem to be of great importance for future work. The methodology proposed in this work could be used to support breeding programs for sheep in progeny tests. References MACQUEEN, J. B. (1967). Some Methods for classification and Analysis of Multivariate Observations.
650 $aDatabases
650 $aInformation retrieval
650 $aBase de Dados
653 $aMarcadores moleculares SNP
653 $aMineração de texto
653 $aRecuperação da informação
653 $aText mining
700 1 $aPAIVA, S. R.
700 1 $aYAMAGISHI, M. E. B.
700 1 $aOLIVEIRA, S. R. de M.
700 1 $aHIGA, R.
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Registro original: |
Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
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Biblioteca |
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| Registros recuperados : 255 | |
| 63. |  | CARDOSO, F. F.; GIACHETTO, P. F.; YAMAGISHI, M. E. B.; HIGA, R. H. Statistical tools to uncover genetic architecture of tick resistance using highdensity oligonucleotide gene expression microarrays. In: SÃO PAULO ADVANCED SCHOOL OF SCIENCE, 1., 2011, São Carlos, SP. Advances in the knowledge of parasite resistance of ruminant hosts and parasites: proceedings. São São Carlos, SP: Embrapa Pecuária Sudeste, 2011. p. 34-38.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sul. |
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| 64. | | LOBO, I.; NASCIMENTO, A.; YAMAGISHI, M.; GUIGUEN, Y.; SILVA, G. F.; ALMEIDA, F. L. The tambaqui (Colossoma macropomum) transcriptome at sex differentiation stage. In: INTERNATIONAL SYMPOSIUM ON REPRODUCTIVE PHYSIOLOGY OF FISH, 11., 2018, Manaus. New fromtiers in reproductive diversity in a changing environment: program and abstracts. [S.l.: s.n.], 2018. p. 90.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Ocidental. |
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| 68. | | HERAI, R.; DITA, M.; WAALWIJK, C.; FERREIRA, G.; SOUZA, M.; KEMA, G.; FALCAO, P.; GIACHETTO, P.; YAMAGISHI, M. Building a transcriptome molecular marker platform for diagnosis of fungal plant pathogens. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 8., 2012, Campinas. Abstract book... Ribeirão Preto: AB3C, 2012. Não paginado. X-MEETING 2012.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 71. | | CHAGAS, S. S.; YAMAGISHI, M. E. B.; ZERLOTINI NETO, A.; SILVA, G. F. da; CANIATO, F. F. Cazymes, peptidases e lipases secretadas do fungo fitopatogênico Pseusopestalotiopsis gilvanii (CPAA222): uma abordagem genômica. In: SIMPÓSIO DE BIOTECNOLOGIA DA UNIVERSIDADE FEDERAL DO AMAZONAS, 1., 2022, Manaus. Anais [recurso eletrônico]: resumos expandidos. Manaus: EDUA, 2022. p. 6.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 72. | | CHAGAS, S. S.; YAMAGISHI, M. E. B.; ZERLOTINI NETO, A.; SILVA, G. F. da; CANIATO, F. F. Cazymes, peptidases e lipases secretadas do fungo fitopatogênico Pseusopestalotiopsis gilvanii (CPAA222): uma abordagem genômica. In: SIMPÓSIO DE BIOTECNOLOGIA DA UNIVERSIDADE FEDERAL DO AMAZONAS, 1., 2022, Manaus. Anais [recurso eletrônico]: resumos expandidos. Manaus: EDUA, 2022. p. 6.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Ocidental. |
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| 73. | | YAMAGISHI, M. E. B.; MARTINS, N. F.; NESHICH, G.; CAI, W.; SHAO, X.; BEAUTRAIT, A.; MAIGRET, B. A fast surface-matching procedure for protein-ligand docking. Journal of Molecular Modeling, v. 12, n. 6, p. 965-972, Sept. 2006.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: -- - A |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 75. | | SOUZA, R. P.; SOUSA, T. F.; QUEIROZ, C. A.; LOPES, E. F.; YAMAGISHI, M. E. B.; SILVA, G. F. da. Identificação de clusters gênicos biossintéticos relacionados a produção de antibióticos em pool bacteriano isolado de sedimentos de rios amazônicos. In: SIMPÓSIO DE BIOTECNOLOGIA DA UNIVERSIDADE FEDERAL DO AMAZONAS, 1., 2022, Manaus. Anais [recurso eletrônico]: resumos expandidos. Manaus: EDUA, 2022. p. 8.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 76. | | SOUZA, R. P.; SOUSA, T. F.; QUEIROZ, C. A.; LOPES, E. F.; YAMAGISHI, M. E. B.; SILVA, G. F. da. Identificação de clusters gênicos biossintéticos relacionados a produção de antibióticos em pool bacteriano isolado de sedimentos de rios amazônicos. In: SIMPÓSIO DE BIOTECNOLOGIA DA UNIVERSIDADE FEDERAL DO AMAZONAS, 1., 2022, Manaus. Anais [recurso eletrônico]: resumos expandidos. Manaus: EDUA, 2022. p. 8.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Ocidental. |
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| 77. | | FALCAO, P. R. K.; YAMAGISHI, M. E. B.; BORRO, L.; MANCINI, A. L.; HIGA, R. H.; NESHICH, G. Identification of folding essential residues by looking at an extensive DB of the structure descriptors in Diamond STING. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 13., 2005, Detroit. Program... Detroit: ISCB, 2005. p. 71. Na publicação: Paula Kuser; Michel Yamagishi; Adauto Mancini; Roberto Higa; Goran Neshich. ISMB 2005. Poster A-47.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 78. | | CASTRO, G. dos S.; SOUSA, T.; YAMAGISHI, M. E. B.; SILVA, G. F. da; GARRETT, R.; SOMAN, L.; KOOLEN, H. Identification of new peptaibols in the strain of Trichoderma amazonicum MMSRG 38A isolated from açaí fruit. In: BRAZILIAN CONFERENCE ON NATURAL PRODUCT (BCNP), 9.; MEETING ON MICROMOLECULAR EVOLUTION, SYSTEMATICS AND ECOLOGY (RESEM), 35., 2023, Salvador. Proceedings [...]. Campinas: Galoá, 2023.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Amazônia Ocidental. |
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| 79. | | GERHARDT, I. R.; GIACHETTO, P. F.; YAMAGISHI, M. E. B.; LOBO, F. P.; TEIXEIRA, J.; PENCHEL, R. M.; MISSIAGGIA, A. Comparative transcriptome analysis of eucalyptus genotypes that differ in carbon allocation. In: INTERNATIONAL PLANT & ANIMAL GENOME, 20., 2012, San Diego. Abstract... Jersey City: Scherago International, 2012. Não paginado. 1 pôster.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Florestas. |
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| 80. | | DITA, M. A.; HERAI, R.; WAALWIJK, C.; YAMAGISHI, M.; GIACHETTO, P.; FERREIRA, G.; SOUZA, M.; KEMA, G. H. J. Comparative transcriptome analysis and genome assembly of Fusarium oxysporum f. sp. cubense. In: INTERNATIONAL PROMUSA SYMPOSIUM, 2011, Salvador. Bananas and plantains: toward sustainable global production and improved uses: abstracts. [S.l.]: ISHS, 2011. p. 58.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| Registros recuperados : 255 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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