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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
26/12/2018 |
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Data da última atualização: |
24/01/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
ALMEIDA, A. L.; SCHETTINO, V. J.; BARBOSA, T. J. R.; FREITAS, P. F.; GUIMARÃES, P. G. S.; ARBEX, W. A. |
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Afiliação: |
WAGNER ANTONIO ARBEX, CNPGL. |
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Título: |
Relative scalability of NoSQL databases for genotype data manipulation. |
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Ano de publicação: |
2018 |
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Fonte/Imprenta: |
Revista de Informática Teórica e Aplicada, v. 25, n. 2, p. 93-100, 2018. |
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DOI: |
10.22456/2175-2745.79334 |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract Genotype data manipulation is one of the greatest challenges in bioinformatics and genomics mainly because of high dimensionality and unbalancing characteristics. These peculiarities explains why Relational Database Management Systems (RDBMSs), the "de facto" standard storage solution, have not been presented as the best tools for this kind of data. However, Big Data has been pushing the development of modern database systems that might be able to overcome RDBMSs deficiencies. In this context, we extended our previous works on the evaluation of relative performance among NoSQLs engines from different families, adapting the schema design in order to achieve better performance based on its conclusions, thus being able to store more SNP markers for each individual. Using Yahoo! Cloud Serving Benchmark (YCSB) benchmark framework, we assessed each database system over hypothetical SNP sequences. Results indicate that although Tarantool has the best overall throughput, MongoDB is less impacted by the increase of SNP markers per individual. |
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Palavras-Chave: |
Data Science; Database; NoSQL; SNP. |
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Thesaurus Nal: |
Bioinformatics; Genotype. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/189325/1/Artigo-RevInfTeorApl-Arbex-Relative.pdf
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Marc: |
LEADER 01813naa a2200265 a 4500
001 2102528
005 2023-01-24
008 2018 bl uuuu u00u1 u #d
024 7 $a10.22456/2175-2745.79334$2DOI
100 1 $aALMEIDA, A. L.
245 $aRelative scalability of NoSQL databases for genotype data manipulation.$h[electronic resource]
260 $c2018
520 $aAbstract Genotype data manipulation is one of the greatest challenges in bioinformatics and genomics mainly because of high dimensionality and unbalancing characteristics. These peculiarities explains why Relational Database Management Systems (RDBMSs), the "de facto" standard storage solution, have not been presented as the best tools for this kind of data. However, Big Data has been pushing the development of modern database systems that might be able to overcome RDBMSs deficiencies. In this context, we extended our previous works on the evaluation of relative performance among NoSQLs engines from different families, adapting the schema design in order to achieve better performance based on its conclusions, thus being able to store more SNP markers for each individual. Using Yahoo! Cloud Serving Benchmark (YCSB) benchmark framework, we assessed each database system over hypothetical SNP sequences. Results indicate that although Tarantool has the best overall throughput, MongoDB is less impacted by the increase of SNP markers per individual.
650 $aBioinformatics
650 $aGenotype
653 $aData Science
653 $aDatabase
653 $aNoSQL
653 $aSNP
700 1 $aSCHETTINO, V. J.
700 1 $aBARBOSA, T. J. R.
700 1 $aFREITAS, P. F.
700 1 $aGUIMARÃES, P. G. S.
700 1 $aARBEX, W. A.
773 $tRevista de Informática Teórica e Aplicada$gv. 25, n. 2, p. 93-100, 2018.
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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Registro |
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Registro Completo
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Biblioteca(s): |
Embrapa Cerrados. |
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Data corrente: |
17/12/2014 |
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Data da última atualização: |
12/02/2015 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 2 |
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Autoria: |
BEZERRA, C. A.; MACEDO, L. L. P.; AMORIM, T. M. L.; SANTOS, V. O.; FRAGOSO, R. da R.; LUCENA, W. A.; MENEGUIM, A. M.; VALENCIA-JIMENEZ, A.; ENGLER, G.; SILVA, M. C. M. da; SA, M. F. G. de; FREIRE, E. V. S. A. |
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Afiliação: |
FURGS; FURGS; RODRIGO DA ROCHA FRAGOSO, CPAC; WAGNER ALEXANDRE LUCENA, CNPA; IAPAR; UNIVERSITY OF CALDAS, COLOMBIA; INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE, FRANCE; MARIA CRISTINA MATTAR DA SILVA, CENARGEN; MARIA FATIMA GROSSI DE SA, CENARGEN; ERIKA VALERIA SALIBA ALBUQUERQUE FR, CENARGEN. |
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Título: |
Molecular cloning and characterization of an a-amylase cDNA highly expressed in major feeding stages of the coffee berry borer, Hypothenemus hampei. |
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Ano de publicação: |
2014 |
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Fonte/Imprenta: |
Gene, v. 553, n. 1, p. 7-16, Dec. 2014. |
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DOI: |
10.1016/j.gene.2014.09.050 |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract: a-Amylases are common enzymes responsible for hydrolyzing starch. Insect-pests, whose larvae develop in seeds, rely obligatorily on a-amylase activity to digest starch, as their major food source. Considering the relevance of insect a-amylases and the natural a-amylase inhibitors present in seeds to protect from insect damage, we report here the molecular cloning and nucleotide sequence of the full-length AmyHha cDNA of the coffee berry borer, Hypothenemus hampei, a major insect-pest of coffee crops. The AmyHha sequence has 1879 bp, containing a 1458 bp open reading frame, which encodes a predicted protein with 485 amino acid residues, with a predicted molecular mass of 51.2 kDa. The deduced protein showed 55?79% identity to other insect a-amylases, including Anthonomus grandis, Ips typographus and Sitophilus oryzae a-amylases. In depth analysis revealed that the highly conserved three amino acid residues (Asp184, Glu220, and Asp285), which compose the catalytic site are also presented in AmyHha amylase. The AmyHha gene seems to be a single copy in the haploid genome and AmyHha transcription levels were found higher in L2 larvae and adult insects, both corresponding to major feeding phases. Modeling of the AmyHha predicted protein uncovered striking structural similarities to the Tenebrio molitor a-amylase also displaying the same amino acid residues involved in enzyme catalysis (Asp184, Glu220 and Asp285). Since AmyHha gene was mostly transcribed in the intestinal tract of H. hampei larvae, the cognate a-amylase could be considered a high valuable target to coffee bean insect control by biotechnological strategies. MenosAbstract: a-Amylases are common enzymes responsible for hydrolyzing starch. Insect-pests, whose larvae develop in seeds, rely obligatorily on a-amylase activity to digest starch, as their major food source. Considering the relevance of insect a-amylases and the natural a-amylase inhibitors present in seeds to protect from insect damage, we report here the molecular cloning and nucleotide sequence of the full-length AmyHha cDNA of the coffee berry borer, Hypothenemus hampei, a major insect-pest of coffee crops. The AmyHha sequence has 1879 bp, containing a 1458 bp open reading frame, which encodes a predicted protein with 485 amino acid residues, with a predicted molecular mass of 51.2 kDa. The deduced protein showed 55?79% identity to other insect a-amylases, including Anthonomus grandis, Ips typographus and Sitophilus oryzae a-amylases. In depth analysis revealed that the highly conserved three amino acid residues (Asp184, Glu220, and Asp285), which compose the catalytic site are also presented in AmyHha amylase. The AmyHha gene seems to be a single copy in the haploid genome and AmyHha transcription levels were found higher in L2 larvae and adult insects, both corresponding to major feeding phases. Modeling of the AmyHha predicted protein uncovered striking structural similarities to the Tenebrio molitor a-amylase also displaying the same amino acid residues involved in enzyme catalysis (Asp184, Glu220 and Asp285). Since AmyHha gene was mostly transcribed in the intestinal... Mostrar Tudo |
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Palavras-Chave: |
Expressão gênica. |
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Thesagro: |
Amido; Curculionideo; Hidrolise; Praga de planta. |
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Thesaurus NAL: |
Curculionidae; Enzymatic hydrolysis; Gene expression; Insect pests; Starch. |
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Categoria do assunto: |
O Insetos e Entomologia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/114033/1/34279.pdf
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Marc: |
LEADER 02768naa a2200385 a 4500
001 2003023
005 2015-02-12
008 2014 bl uuuu u00u1 u #d
024 7 $a10.1016/j.gene.2014.09.050$2DOI
100 1 $aBEZERRA, C. A.
245 $aMolecular cloning and characterization of an a-amylase cDNA highly expressed in major feeding stages of the coffee berry borer, Hypothenemus hampei.
260 $c2014
520 $aAbstract: a-Amylases are common enzymes responsible for hydrolyzing starch. Insect-pests, whose larvae develop in seeds, rely obligatorily on a-amylase activity to digest starch, as their major food source. Considering the relevance of insect a-amylases and the natural a-amylase inhibitors present in seeds to protect from insect damage, we report here the molecular cloning and nucleotide sequence of the full-length AmyHha cDNA of the coffee berry borer, Hypothenemus hampei, a major insect-pest of coffee crops. The AmyHha sequence has 1879 bp, containing a 1458 bp open reading frame, which encodes a predicted protein with 485 amino acid residues, with a predicted molecular mass of 51.2 kDa. The deduced protein showed 55?79% identity to other insect a-amylases, including Anthonomus grandis, Ips typographus and Sitophilus oryzae a-amylases. In depth analysis revealed that the highly conserved three amino acid residues (Asp184, Glu220, and Asp285), which compose the catalytic site are also presented in AmyHha amylase. The AmyHha gene seems to be a single copy in the haploid genome and AmyHha transcription levels were found higher in L2 larvae and adult insects, both corresponding to major feeding phases. Modeling of the AmyHha predicted protein uncovered striking structural similarities to the Tenebrio molitor a-amylase also displaying the same amino acid residues involved in enzyme catalysis (Asp184, Glu220 and Asp285). Since AmyHha gene was mostly transcribed in the intestinal tract of H. hampei larvae, the cognate a-amylase could be considered a high valuable target to coffee bean insect control by biotechnological strategies.
650 $aCurculionidae
650 $aEnzymatic hydrolysis
650 $aGene expression
650 $aInsect pests
650 $aStarch
650 $aAmido
650 $aCurculionideo
650 $aHidrolise
650 $aPraga de planta
653 $aExpressão gênica
700 1 $aMACEDO, L. L. P.
700 1 $aAMORIM, T. M. L.
700 1 $aSANTOS, V. O.
700 1 $aFRAGOSO, R. da R.
700 1 $aLUCENA, W. A.
700 1 $aMENEGUIM, A. M.
700 1 $aVALENCIA-JIMENEZ, A.
700 1 $aENGLER, G.
700 1 $aSILVA, M. C. M. da
700 1 $aSA, M. F. G. de
700 1 $aFREIRE, E. V. S. A.
773 $tGene$gv. 553, n. 1, p. 7-16, Dec. 2014.
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Embrapa Cerrados (CPAC) |
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