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 | Acesso ao texto completo restrito à biblioteca da Embrapa Agricultura Digital. Para informações adicionais entre em contato com cnptia.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
23/08/2012 |
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Data da última atualização: |
08/01/2020 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
LOBO, F. P.; RODRIGUES, M. R.; RODRIGUES, G. O. L.; HILÁRIO, H. O.; SOUZA, R. A.; TAUCH, A.; MIYOSHI, A.; FRANCO, G. C.; AZEVEDO, V.; FRANCO, G. R. |
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Afiliação: |
FRANCISCO PEREIRA LOBO, CNPTIA; MAÍRA R. RODRIGUES, UFMG; GISELE O. L. RODRIGUES, UFMG; HERON O. HILÁRIO, UFMG; RAONI A. SOUZA, Fundação Ezequiel Dias, MG; ANDREAS TAUCH, Bielefeld University; ANDERSON MIYOSHI, UFMG; GLAURA C. FRANCO, UFMG; VASCO AZEVEDO, UFMG; GLÓRIA R. FRANCO, UFMG. |
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Título: |
KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa. |
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Ano de publicação: |
2012 |
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Fonte/Imprenta: |
Nucleic Acids Research, Oxford, v. 40, p. W491-W497, 2012. |
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DOI: |
10.1093/nar/gks490 |
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Idioma: |
Inglês |
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Conteúdo: |
The enrichment analysis is a standard procedure to interpret ?omics? experiments that generate large gene lists as outputs, such as transcriptomics and protemics. However, despite the huge success of enrichment analysis in these classes of experiments, there is a surprising lack of application of this methodology to survey other categories of large-scale biological data available. Here, we report Kegg Orthology enrichMent-Online DetectiOn (KOMODO), a web tool to systematically investigate groups of monophyletic genomes in order to detect significantly enriched groups of homologous genes in one taxon when compared with another. The results are displayed in their proper biochemical roles in a visual, explorative way, allowing users to easily formulate and investigate biological hypotheses regarding the taxonomical distribution of genomic elements. We validated KOMODO by analyzing portions of central carbon metabolism in two taxa extensively studied regarding their carbon metabolism profile (Enterobacteriaceae family and Lactobacillales order). Most enzymatic activities significantly biased were related to known key metabolic traits in these taxa, such as the distinct fates of pyruvate (the known tendency of lactate production in Lactobacillales and its complete oxidation in Enterobacteriaceae), demonstrating that KOMODO could detect biologically meaningful differences in the frequencies of shared genomic elements among taxa. KOMODO is freely available at http://komodotool.org. |
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Palavras-Chave: |
Bioinformática; Ferramenta web; Genomas. |
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Thesagro: |
Atividade Enzimática. |
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Thesaurus Nal: |
Bioinformatics; Genome. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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Marc: |
LEADER 02413naa a2200313 a 4500
001 1932006
005 2020-01-08
008 2012 bl uuuu u00u1 u #d
024 7 $a10.1093/nar/gks490$2DOI
100 1 $aLOBO, F. P.
245 $aKOMODO$ba web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa.$h[electronic resource]
260 $c2012
520 $aThe enrichment analysis is a standard procedure to interpret ?omics? experiments that generate large gene lists as outputs, such as transcriptomics and protemics. However, despite the huge success of enrichment analysis in these classes of experiments, there is a surprising lack of application of this methodology to survey other categories of large-scale biological data available. Here, we report Kegg Orthology enrichMent-Online DetectiOn (KOMODO), a web tool to systematically investigate groups of monophyletic genomes in order to detect significantly enriched groups of homologous genes in one taxon when compared with another. The results are displayed in their proper biochemical roles in a visual, explorative way, allowing users to easily formulate and investigate biological hypotheses regarding the taxonomical distribution of genomic elements. We validated KOMODO by analyzing portions of central carbon metabolism in two taxa extensively studied regarding their carbon metabolism profile (Enterobacteriaceae family and Lactobacillales order). Most enzymatic activities significantly biased were related to known key metabolic traits in these taxa, such as the distinct fates of pyruvate (the known tendency of lactate production in Lactobacillales and its complete oxidation in Enterobacteriaceae), demonstrating that KOMODO could detect biologically meaningful differences in the frequencies of shared genomic elements among taxa. KOMODO is freely available at http://komodotool.org.
650 $aBioinformatics
650 $aGenome
650 $aAtividade Enzimática
653 $aBioinformática
653 $aFerramenta web
653 $aGenomas
700 1 $aRODRIGUES, M. R.
700 1 $aRODRIGUES, G. O. L.
700 1 $aHILÁRIO, H. O.
700 1 $aSOUZA, R. A.
700 1 $aTAUCH, A.
700 1 $aMIYOSHI, A.
700 1 $aFRANCO, G. C.
700 1 $aAZEVEDO, V.
700 1 $aFRANCO, G. R.
773 $tNucleic Acids Research, Oxford$gv. 40, p. W491-W497, 2012.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Biblioteca(s): |
Embrapa Meio Ambiente. |
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Data corrente: |
11/02/2016 |
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Data da última atualização: |
18/03/2016 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
PESSOA, M. C. P. Y.; FRASCÁ-SCORVO, C. M. D.; LOSEKANN, M. E.; HISANO, H.; SCORVO FILHO, J.; SILVA, C. A. da; SILVA, M. S. G. M. e; SAMPAIO, F. G.; INOUE, L. A. K. A.; BERGAMIN, G. T.; QUEIROZ, J. F. de; PAZZIANOTTO, C. B. |
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Afiliação: |
MARIA CONCEICAO PERES YOUNG PESSOA, CNPMA; C. M. D. FRASCÁ-SCORVO, APTA; MARCOS ELISEU LOSEKANN, CNPMA; HAMILTON HISANO, CNPMA; J. D. SCORVO FILHO, APTA; C. A. SILVA; MARIANA SILVEIRA GUERRA MOURA E SILVA, CNPMA; FERNANDA GARCIA SAMPAIO, CNPMA; L. A. K. A. INOUE; G. T. BERGAMIN; JULIO FERRAZ DE QUEIROZ, CNPMA; CARLOS BENJAMIN PAZZIANOTTO, CNPMA. |
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Título: |
Aquisys 1.3 - validated version of the computer system to support best management practices (BMP) and environmental management for aquaculture in Brazil. |
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Ano de publicação: |
2015 |
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Fonte/Imprenta: |
In: FENACAM & LACQUA/SARA (WAS)?15, 2015, Fortaleza. Science & Industry joining forces to meet seafood demands: abstracts... Fortaleza: ABCC; World Aquaculture Society, 2015. |
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Páginas: |
210 |
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Idioma: |
Inglês |
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Conteúdo: |
The present work presents the validated version of the computer system to support Best Management Practices (BPM) and Environmental Management for aquaculture in Brazil ? Aquisys 1.3, resulting from Aquisys Validation Project conducted by Embrapa Environment. The prototype version, Aquisys 1.0, developed in the ?Management and Environmental Management of Aquiculture? Project (?Aquabrasil? network Project) makes use of information acquired by the user via visual observations, low cost water quality kits and common samples held on the farm. This data is input in the system in a questionnaire, which will enable the system to manage this information and provide the user with necessary guidance, assessment and calculations to achieve best manage practice and streamlinedproductivity. Aquisys 1.0 was presented and evaluated by different users like fish farmers, aquaculture researchers, technical extensionists, aquaculture post-graduation and graduation students, among others. Its access, guidance and calculation features have had their results observed, specially focusing on the routine for tilapia production system in order to make it fitted to Brazilian different regional characteristics. The evaluations consider characteristics both of properties and of production place. They also took into account given indicators of management and production, of water quality, and of economical profitability. The validated version, Aquisys 1.3, enabled significant updates on the production system options turning available, both rapidly and in an appropriate language, information ready to use, and enabling a rapidly access both to information, guidance of a minimum set of BPM and Environmental practices and calculations, initially focusing on pond production system. Aquisys 1.3 is a systematic unpaid and on-line available on the Internet at http://www.cnpma.embrapa.br/aquisys. As an indicatory system its use does not exclude the necessity of qualified professional monitoring for more precise diagnoses. MenosThe present work presents the validated version of the computer system to support Best Management Practices (BPM) and Environmental Management for aquaculture in Brazil ? Aquisys 1.3, resulting from Aquisys Validation Project conducted by Embrapa Environment. The prototype version, Aquisys 1.0, developed in the ?Management and Environmental Management of Aquiculture? Project (?Aquabrasil? network Project) makes use of information acquired by the user via visual observations, low cost water quality kits and common samples held on the farm. This data is input in the system in a questionnaire, which will enable the system to manage this information and provide the user with necessary guidance, assessment and calculations to achieve best manage practice and streamlinedproductivity. Aquisys 1.0 was presented and evaluated by different users like fish farmers, aquaculture researchers, technical extensionists, aquaculture post-graduation and graduation students, among others. Its access, guidance and calculation features have had their results observed, specially focusing on the routine for tilapia production system in order to make it fitted to Brazilian different regional characteristics. The evaluations consider characteristics both of properties and of production place. They also took into account given indicators of management and production, of water quality, and of economical profitability. The validated version, Aquisys 1.3, enabled significant updates on the production sys... Mostrar Tudo |
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Palavras-Chave: |
Aquafarming; Best Aquaculture Practices (BAP); Web system. |
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Thesagro: |
Oreochromis Niloticus. |
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Thesaurus NAL: |
Aquaculture; Fisheries; Good aquaculture practices. |
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Categoria do assunto: |
A Sistemas de Cultivo |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/138734/1/2015RA-059.pdf
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Marc: |
LEADER 03203nam a2200337 a 4500
001 2036546
005 2016-03-18
008 2015 bl uuuu u00u1 u #d
100 1 $aPESSOA, M. C. P. Y.
245 $aAquisys 1.3 - validated version of the computer system to support best management practices (BMP) and environmental management for aquaculture in Brazil.$h[electronic resource]
260 $aIn: FENACAM & LACQUA/SARA (WAS)?15, 2015, Fortaleza. Science & Industry joining forces to meet seafood demands: abstracts... Fortaleza: ABCC; World Aquaculture Society$c2015
300 $a210
520 $aThe present work presents the validated version of the computer system to support Best Management Practices (BPM) and Environmental Management for aquaculture in Brazil ? Aquisys 1.3, resulting from Aquisys Validation Project conducted by Embrapa Environment. The prototype version, Aquisys 1.0, developed in the ?Management and Environmental Management of Aquiculture? Project (?Aquabrasil? network Project) makes use of information acquired by the user via visual observations, low cost water quality kits and common samples held on the farm. This data is input in the system in a questionnaire, which will enable the system to manage this information and provide the user with necessary guidance, assessment and calculations to achieve best manage practice and streamlinedproductivity. Aquisys 1.0 was presented and evaluated by different users like fish farmers, aquaculture researchers, technical extensionists, aquaculture post-graduation and graduation students, among others. Its access, guidance and calculation features have had their results observed, specially focusing on the routine for tilapia production system in order to make it fitted to Brazilian different regional characteristics. The evaluations consider characteristics both of properties and of production place. They also took into account given indicators of management and production, of water quality, and of economical profitability. The validated version, Aquisys 1.3, enabled significant updates on the production system options turning available, both rapidly and in an appropriate language, information ready to use, and enabling a rapidly access both to information, guidance of a minimum set of BPM and Environmental practices and calculations, initially focusing on pond production system. Aquisys 1.3 is a systematic unpaid and on-line available on the Internet at http://www.cnpma.embrapa.br/aquisys. As an indicatory system its use does not exclude the necessity of qualified professional monitoring for more precise diagnoses.
650 $aAquaculture
650 $aFisheries
650 $aGood aquaculture practices
650 $aOreochromis Niloticus
653 $aAquafarming
653 $aBest Aquaculture Practices (BAP)
653 $aWeb system
700 1 $aFRASCÁ-SCORVO, C. M. D.
700 1 $aLOSEKANN, M. E.
700 1 $aHISANO, H.
700 1 $aSCORVO FILHO, J.
700 1 $aSILVA, C. A. da
700 1 $aSILVA, M. S. G. M. e
700 1 $aSAMPAIO, F. G.
700 1 $aINOUE, L. A. K. A.
700 1 $aBERGAMIN, G. T.
700 1 $aQUEIROZ, J. F. de
700 1 $aPAZZIANOTTO, C. B.
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