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Registro Completo |
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Biblioteca(s): |
Embrapa Soja. |
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Data corrente: |
07/04/2004 |
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Data da última atualização: |
27/07/2007 |
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Autoria: |
BINNECK, E.; SILVA, J. F. V.; NEUMAIER, N.; FARIAS, J. R. B.; ARIAS, C. A. A.; ALMEIDA, A. M. R.; MARIN, S. R. R.; WENDLAND, A.; SILVEIRA, C. A. da; MOLINA, J. C.; LEMOS, N. G.; FUGANTI, R.; STOLF, R.; NEPOMUCENO, A. L. |
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Título: |
Bioinformatics tools for sequence analysis and annotation applied to soybean functional genome. |
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Ano de publicação: |
2004 |
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Fonte/Imprenta: |
In: WORLD SOYBEAN RESEARCH CONFERENCE, 7.; INTERNATIONAL SOYBEAN PROCESSING AND UTILIZATION CONFERENCE, 4.; CONGRESSO BRASILEIRO DE SOJA, 3., 2004, Foz do Iguassu. Abstracts of contributed papers and posters. Londrina: Embrapa Soybean, 2004. |
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Páginas: |
p. 248-249. |
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Série: |
(Embrapa Soja. Documentos, 228). |
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Idioma: |
Inglês |
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Notas: |
Editado por Flávio Moscardi, Clara Beatriz Hoffmann-Campo, Odilon Ferreira Saraiva, Paulo Roberto Galerani, Francisco Carlos Krzyzanowski, Mercedes Concordia Carrão-Panizzi. |
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Conteúdo: |
Worldwide functional genomics studies are making an important role on biotechnology for the identification of genes that can be use in the improvement of specific biological processes in plants. Large-scale gene discovery projects like that depend on high accuracy of the data. The data should not only be trustworthy but should be correctly annotated for various features it contains. In this work we report a bioinformatics system designed to process and annotate the expressed sequence tags (ESTs) obtained by the project Functional Genome of Soybean Roots at Embrapa Soybean (http://www.cnpso.embrapa.br/bioinformatica). The system is made of Perl and PHP scripts, which performs the automated sequence analysis and support the annotation process based on a MySQL database. Various Perl scripts was written to assist the sequence analysis process that includes basecalling, clustering and assembling the reads, filtering of contaminating, repetitive and low quality sequences, identification of sequence features, BLASTing and reports generation. BLAST (Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402) outputs are processed and disposed on a way that is easily accessed by the personal that performs the massive handle of the data for annotation. Also, PHP scripts was written to make a friendly annotation interface through dynamical Web pages that perform the database operations needed for the complete annotation of the genes, whish comprise data retrieval aided by query searches linked to key words, data insertion, update, and generation of intuitive reports describing the results. These tools are helping to direct our work on identification, cloning and characterization of genes and regulatory sequences potentially useful in the improvement of soybean through genetic engineering. As results nearly 8,000 ESTs was obtained form cDNA clones derived from soybean roots in drought stress and nematode infection conditions. Consensus sequences are being functionally annotated and used to construct cDNA microarrays that will be useful for analyze gene expression under a broad variety of conditions. Initially we are studying drought stress and nematode infection conditions. Analysis of interactions of soybean roots with this defiance conditions will be used do identify new possible sources of resistance and tolerance. Candidate genes will be deeply studied and can be used on the production of transgenic plants. This work was supported by grants from CNPq, PRODETAB, Jircas and Embrapa. MenosWorldwide functional genomics studies are making an important role on biotechnology for the identification of genes that can be use in the improvement of specific biological processes in plants. Large-scale gene discovery projects like that depend on high accuracy of the data. The data should not only be trustworthy but should be correctly annotated for various features it contains. In this work we report a bioinformatics system designed to process and annotate the expressed sequence tags (ESTs) obtained by the project Functional Genome of Soybean Roots at Embrapa Soybean (http://www.cnpso.embrapa.br/bioinformatica). The system is made of Perl and PHP scripts, which performs the automated sequence analysis and support the annotation process based on a MySQL database. Various Perl scripts was written to assist the sequence analysis process that includes basecalling, clustering and assembling the reads, filtering of contaminating, repetitive and low quality sequences, identification of sequence features, BLASTing and reports generation. BLAST (Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402) outputs are processed and disposed on a way that is easily accessed by the personal that performs the massive handle of the data for annotation. Also, PHP scripts was written to make a friendly annotation interface through dynamical Web pages that perform the database operations needed for the complete annotation of the genes, whish comprise data retrieval aided by query searches li... Mostrar Tudo |
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Categoria do assunto: |
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Marc: |
LEADER 03743naa a2200313 a 4500
001 1466823
005 2007-07-27
008 2004 bl uuuu u00u1 u #d
100 1 $aBINNECK, E.
245 $aBioinformatics tools for sequence analysis and annotation applied to soybean functional genome.
260 $c2004
300 $ap. 248-249.
490 $a(Embrapa Soja. Documentos, 228).
500 $aEditado por Flávio Moscardi, Clara Beatriz Hoffmann-Campo, Odilon Ferreira Saraiva, Paulo Roberto Galerani, Francisco Carlos Krzyzanowski, Mercedes Concordia Carrão-Panizzi.
520 $aWorldwide functional genomics studies are making an important role on biotechnology for the identification of genes that can be use in the improvement of specific biological processes in plants. Large-scale gene discovery projects like that depend on high accuracy of the data. The data should not only be trustworthy but should be correctly annotated for various features it contains. In this work we report a bioinformatics system designed to process and annotate the expressed sequence tags (ESTs) obtained by the project Functional Genome of Soybean Roots at Embrapa Soybean (http://www.cnpso.embrapa.br/bioinformatica). The system is made of Perl and PHP scripts, which performs the automated sequence analysis and support the annotation process based on a MySQL database. Various Perl scripts was written to assist the sequence analysis process that includes basecalling, clustering and assembling the reads, filtering of contaminating, repetitive and low quality sequences, identification of sequence features, BLASTing and reports generation. BLAST (Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402) outputs are processed and disposed on a way that is easily accessed by the personal that performs the massive handle of the data for annotation. Also, PHP scripts was written to make a friendly annotation interface through dynamical Web pages that perform the database operations needed for the complete annotation of the genes, whish comprise data retrieval aided by query searches linked to key words, data insertion, update, and generation of intuitive reports describing the results. These tools are helping to direct our work on identification, cloning and characterization of genes and regulatory sequences potentially useful in the improvement of soybean through genetic engineering. As results nearly 8,000 ESTs was obtained form cDNA clones derived from soybean roots in drought stress and nematode infection conditions. Consensus sequences are being functionally annotated and used to construct cDNA microarrays that will be useful for analyze gene expression under a broad variety of conditions. Initially we are studying drought stress and nematode infection conditions. Analysis of interactions of soybean roots with this defiance conditions will be used do identify new possible sources of resistance and tolerance. Candidate genes will be deeply studied and can be used on the production of transgenic plants. This work was supported by grants from CNPq, PRODETAB, Jircas and Embrapa.
700 1 $aSILVA, J. F. V.
700 1 $aNEUMAIER, N.
700 1 $aFARIAS, J. R. B.
700 1 $aARIAS, C. A. A.
700 1 $aALMEIDA, A. M. R.
700 1 $aMARIN, S. R. R.
700 1 $aWENDLAND, A.
700 1 $aSILVEIRA, C. A. da
700 1 $aMOLINA, J. C.
700 1 $aLEMOS, N. G.
700 1 $aFUGANTI, R.
700 1 $aSTOLF, R.
700 1 $aNEPOMUCENO, A. L.
773 $tIn: WORLD SOYBEAN RESEARCH CONFERENCE, 7.; INTERNATIONAL SOYBEAN PROCESSING AND UTILIZATION CONFERENCE, 4.; CONGRESSO BRASILEIRO DE SOJA, 3., 2004, Foz do Iguassu. Abstracts of contributed papers and posters. Londrina: Embrapa Soybean, 2004.
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Registro original: |
Embrapa Soja (CNPSO) |
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Biblioteca |
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Tipo/Formato |
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| Registros recuperados : 201 | |
| 141. |  | AZÊVEDO, H. S. F. da S.; AZEVEDO, J. M. A. de; ROCHA, A. A. da; WADT, L. H. de O.; CAMPOS, T. de. Extrativismo do açaizeiro Euterpe precatoria Mart. no Acre. In: SIVIERO, A.; SANTOS, R. C. dos; MATTAR, E. P. L. (Org.). Conservação e tecnologias para o desenvolvimento agrícola e florestal no Acre. Rio Branco, AC: Ifac, 2019. Cap. 5, p. 147-172.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Acre; Embrapa Rondônia. |
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| 142. | | PAULA, V. G. de; SOUSA, R. S. de; SILVA, R. C. M. R. da; ALVES, E. G.; CAETANO, A. R.; IANELLA, P.; CAMPOS, T. A. de. fim3–24/ptxP-3 genotype is associated to whooping cough outbreak in Brazilian Midwest: The selection of Bordetella pertussis strains driven by vaccine immunization. Infection, Genetics and Evolution, v. 121, 105599, 2024.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 143. | | RUFINO, P. B.; OLIVEIRA, J. C. de; AZEVEDO, H. N. de; SOUZA, E. C. de; SILVA, L. M. da; ASSIS, G. M. L. de; CAMPOS, T. de. Estimativa de taxa de cruzamento em Arachis pintoi com marcadores microssatélites. In: CONGRESSO REGIONAL DE PESQUISA DO ESTADO DO ACRE; SEMINÁRIO DE INICIAÇÃO CIENTÍFICA DA UFAC, 24., 2015, Rio Branco. Anais... Rio Branco: CNPq; Ufac; Embrapa; Fapac; Ieval, 2015. 1 p.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Acre. |
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| 144. | | OLIVEIRA, J. C. de; RUFINO, P. B.; AZÊVEDO, H. S. F. da S.; ASSIS, G. M. L. de; SOUSA, A. C. B. de; CAMPOS, T. de. Estimativa da reprodução cruzada em amendoim forrageiro usando microssatélites. In: CONGRESSO REGIONAL DE PESQUISA DO ESTADO DO ACRE; SEMINÁRIO DE INICIAÇÃO CIENTÍFICA DA UFAC, 24., 2015, Rio Branco. Anais... Rio Branco: CNPq; Ufac; Embrapa; Fapac; Ieval, 2015. 1 p.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Acre. |
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| 145. | | ANDRADE, A. G. de; PORTOCARRERO, H.; CHAVES, T. de A.; LIMA, J. A. de S.; BARROSO, D. G.; CAMPOS, T. M. P. de. Manejo de solo, água, planta e resíduo para o controle da erosão e recuperação de áreas degradadas. In: SEMINÁRIO DA REDE AGROHIDRO, 1., 2012, Rio de Janeiro. Água: desafios para a sustentabilidade da agricultura: anais. Rio de Janeiro: Embrapa Solos, 2014. p. 52-54.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Solos. |
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| 146. | | IANELLA, P.; CAMPOS, T. A. de; PAIVA, S. R.; GUIMARAES, M. F. M.; SILVA, M. V. G. B.; CAETANO, A. R. Prospecção de Polimorfismos de Base Única (SNPs) no gene k-caseina (KCN) na raça Girolando. In: REUNIÃO ANUAL DA SOCIEDADE BRASILEIRA DE ZOOTECNIA, 47., 2010, Salvador. Empreendedorismo e progresso científico na zootecnia brasileira: anais. Viçosa, MG: Sociedade Brasileira de Zootecnia, 2010. 3 p.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Gado de Leite; Embrapa Recursos Genéticos e Biotecnologia. |
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| 149. | | SANTIAGO-NETO, W.; MACHADO, G.; PAIM, D. S.; CAMPOS, T. de; BRITO, M. A. V. P. e; CARDOSO, M. R. I.; CORBELLINI, L. G. Relação da idade na presença de bactérias resistentes a antimicrobianos em rebanhos leiteiros no Rio Grande do Sul. Pesquisa Veterinária Brasileira, v. 34, n. 7, p. 613-620, 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Gado de Leite. |
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| 150. | | ROGGIA, S.; PASINI, A.; LOFEGO, A. C.; SISMEIRO, M. N. S.; CAMPOS, T. A.; SILVA, J. E. P.; OLIVEIRA, M. F. Soja Bt: flutuação de pragas e predadores. In: SIMPÓSIO DE CONTROLE BIOLÓGICO, 13., 2013, Bonito, MS. Anais... Brasília, DF: Embrapa, 2013. 1 CD-ROM. SICONBIOL.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 151. | | SILVA, A. L. D. da; ALVES FILHO, E. G.; SILVA, L. M. A. e; TAVARES, O. C. H.; PEREIRA, M. G.; CAMPOS, T. de; SILVA, L. M. da. Near infrared spectroscopy to rapid assess the rubber tree clone and the influence of maturation and disease at the leaves. Microchemical Journal, v. 168, 106478, Sept. 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Acre; Embrapa Agroindústria Tropical. |
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| 152. | | SOUSA, A. C. B. de; CARVALHO, M. A.; CAMPOS, T. de; SILVA, G. de T. e; ZUCCHI, M. I.; JANK, L.; ANETE PEREIRA DE SOUZA. Outcrossing Rate in Calopogonium mucunoides Desv. Based on Microsatellite Markers. In: INTERNATIONAL SYMPOSIUM ON FORAGE BREEDING, 3., 2011, Bonito, MS. Breeding forage for climate change adaptation and mitigation - eco-efficient animal produtction: proceedings. [Campo Grande, MS: Embrapa Gado de Corte], 2011. 6-9 1 CD-ROM| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Gado de Corte. |
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| 153. | | AZÊVEDO, H. S. F. da S.; RUFINO, P. B.; AZEVEDO, J. M. A. de; SILVA, L. M. da; WADT, L. H. de O.; CAMPOS, T. de. Preservation and maceration of amazon açai leaflet Tissue to obtain genomic DNA. Bioscience Journal, Uberlândia, v. 35, n. 4, p. 1188-1197, July/Aug. 2019.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Acre; Embrapa Rondônia. |
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| 154. | | ROSA, P. M.; CAMPOS, T. de; SOUSA, A. C. B. de; SFORÇA, D. A.; TORRES, G. A. M.; SOUZA, A. P. de. Potato cultivar identification using molecular markers. Pesquisa Agropecuária Brasileira, Brasília, DF, v. 45, n. 1, p. 110-113, jan. 2010. Notas Científicas.
Título em português: Identificação de cultivares de batata por marcadores moleculares.| Biblioteca(s): Embrapa Unidades Centrais. |
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| 155. | | SOUSA, A. C. B.; CARVALHO, M. A.; BOAVENTURA, L. R.; SFORÇA, D. A.; CAMPOS, T.; JUNGMANN, L. J.; ZUCCHI, M. I.; JANK, L.; SOUZA, A. P. Microsatellite markers in tropical legume (Centrosema pubescens Benth): development, characterization, and cross-species amplification in Centrosema sp. Conservation Genetics Resources, v. 1, n.1, p. 347-352, Dec. 2009.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 4 |
| Biblioteca(s): Embrapa Gado de Corte. |
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| 156. | | SOUSA, A. C. B. de; CAMPOS, T. de; SFORÇA, D. A.; JUNGMANN, L.; ZUCCHI, M. I.; JANK, L.; SOUZA, A. P. de. Microsatellite markers in molecular characterization of germplasm bank of Panicum maximum Jacq. In:SIMPÓSIO INTERNACIONAL SOBRE MELHORAMENTO DE FORRAGEIRAS, 2., 2009, Campo Grande, MS. [Anais]... Campo Grande, MS: Embrapa Gado de Corte, 2009. II SIMF. Comitê editorial: Liana Jank; Lucimara Chiari; Rosângela Maria Simeão Resende. 4 p. 1 CD-ROM. Resumo. B 02.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Gado de Corte. |
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| 157. | | SOUZA, E. C. B. de; CAMPOS, T. de; SFORÇA, D. A.; JUNGMANN, L.; ZUCCHI, M. I.; JANK, L.; SOUZA, A. P. de. Microsatellite markers in Panicum maximum Jacq. (Poaceae): a study for the genetic diversity, Germoplasm conservation and breeding. In: JANK, L.; CHIARI, L.; VALLE, C. B. do; RESENDE, R. M. S. (Ed.). Forage breeding and biotechnology. Brasília, DF: Embrapa; Campo Grande: Embrapa Gado de Corte, 2013. p. 195-211.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Gado de Corte. |
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| 158. | | SOUSA, A. C. B. de; CAMPOS, T. de; SFORÇA, D. A.; JUNGMANN, L.; ZUCCHI, M. I.; JANK, L.; SOUZA, A. P. de. Microsatellite markers in Panicum maximum Jacq. (Poaceae): a study for the genetic diversity, germplasm conservation and breeding. In:SIMPÓSIO INTERNACIONAL SOBRE MELHORAMENTO DE FORRAGEIRAS, 2., 2009, Campo Grande, MS. [Anais]... Campo Grande, MS: Embrapa Gado de Corte, 2009. II SIMF. Comitê editorial: Liana Jank; Lucimara Chiari; Rosângela Maria Simeão Resende. 14 p. 1 CD-ROM. Palestra. P 12.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Gado de Corte. |
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| 159. | | SOUSA, A. C. B. de; CAMPOS, T. de; SFORÇA, D. A.; JUNGMANN, L.; ZUCCHI, M. I.; JANK, L.; SOUZA, A. P. de. Microsatellite markers in Panicum maximum Jacq. (Poaceae): a study for the genetic diversity, germplasm conservation an breeding. In: JANK, L.; CHIARI, L.; VALLE, C. B. DO; SIMEÃO, R. M. Forage breeding and biotechnology. Brasília, DF: Embrapa, 2013. p. 195-211.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Acre. |
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| 160. | | SOUSA, A. C. B.; CARVALHO, M. A.; BOAVENTURA, L. R.; SFORÇA, D. A.; CAMPOS, T.; CANCADO, L. J.; ZUCCHI, M. I.; JANK, L.; SOUZA, A. P. Microsatellite markers in tropical legume (Centrosema pubescens Benth): development, characterization, and cross-species amplification in Centrosema sp. Conservation Genetics Resources, v. 1, p. 347-352, 2009.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 4 |
| Biblioteca(s): Embrapa Cerrados. |
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| Registros recuperados : 201 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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