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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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| Registros recuperados : 218 | |
| 201. |  | NEPOMUCENO, A. L.; FARIAS, J. R. B.; YAMAGUCHI-SHINOZAKI, K.; BENEVENTI, M. A.; NEUMAIER, N.; YAMANAKA, N.; NAKASHIMA, K.; BINNECK, E.; MARIN, S. R. R.; STOLF, R.; FUGANTI, R.; SILVEIRA, C. A. da; OLIVEIRA, M. C. N. de; ABDELNOOR, R. V.; ROLLA, A. A. P.; POLIZEL, A. M. Introdução de genes por biobalística em soja visando tolerância à seca. In: SARAIVA, O. F.; LEITE, R. M. V. B. de C. (Ed.). Resultados de pesquisa da Embrapa Soja 2006. Londrina: Embrapa Soja, 2008. p. 109-124. (Embrapa Soja. Documentos, 308).| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Soja. |
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| 202. | | BENEVENTI, M. A.; NAKASHIMA, K.; YAMANAKA, N.; BINNECK, E.; FARIAS, J. R. B.; OLIVEIRA, M. C. N.; NEUMAIER, N.; ABDELNOOR, R. V.; MARCELINO, F. C.; MARIN, S. R. R.; SILVEIRA, C. A.; FUGANTI R.; STOLF, R.; SALINET, L.; ROLLA, A. A. P.; POLIZEL, A. M.; YAMAGUCHI-SHINOZAKI, K.; NEPOMUCENO, A. L. Introduction of Arabidopsis thaliana DREB1A/CBF3 transcription factor into soybean improves drought stress tolerance. In: INTERNATIONAL CONFERENCE ON INTEGRATED APPROACHES TO IMPROVE CROP PRODUCTION UNDER DROUGHT-PRONE ENVIRONMENTS, 3., 2009, Shangai. Abstracts... Shangai: Shangai Academy of Agricultural Sciences: Shangai Agrobiological Gene Center, 2009. p. 133, ref. P 4.07. INTERDROUGHT 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 203. | | POLIZEL, A. M.; MEDRI, M. E.; NAKASHIMA, K.; YAMANAKA, N.; FARIAS, J. R. B.; OLIVEIRA, M. C. N. de; MARIN, S. R. R.; ABDELNOOR, R. V.; MARCELINO, F. C.; FUGANTI, R.; RODRIGUES, F. A.; STOLF-MOREIRA, R.; BENEVENTI, M. A.; ROLLA, A. A. P.; NEUMAIER, N.; YAMAGUCHI-SHINOZAKI, K.; CARVALHO, J. F. C.; NEPOMUCENO, A. L. Molecular, anatomical and physiological properties of a genetically modified soybean line transformed with rd29A:AtDREB1A for the improvement of drought tolerance. Genetics and Molecular Research, Ribeirão Preto, v. 10, n. 4, p. 3641-3656, 2011.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Soja. |
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| 204. | | FUGANTI, R.; ENGELS, C.; RODRIGUES, F. A.; MARINHO, J. P.; LEITE, J. P.; GIROTTO, L.; MOLINARI, M. D. C.; KANAMORI, N.; MARIN, S. R. R.; FARIAS, J. R. B.; NEUMAIER, N.; OLIVEIRA, M. C. N. de; MARCELINO, F. C.; MIZOI, J.; YAMAGUCHI-SHINOZAKI, K.; NEPOMUCENO, A. L. Molecular characterization by qPCR of Soybean (Glycine max L. Merril) genetically modified lines expressing AtDREB2A gene, submitted to water stress treatments. In: CONGRESSO BRASILEIRO DE BIOTECNOLOGIA, 3., 2010, Fortaleza. Programa e resumos. Brasília, DF: SBBiotec, 2010. p. 188-189.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 205. | | ENGELS, C.; FUGANTI, R.; RODRIGUES, F. A.; GIROTTO, L.; SANCHES B. B.; LEITE J. P.; ROLLA, A. A. P.; MARIN, S. R. R.; SILVEIRA, C. A.; FARIAS, J. R. B.; MARCELINO, F. C.; ABDELNOOR, R. V.; SHINOZAKI, K.; NEPOMUCENO, A. L. Obtenção e caracterização de plantas de soja (Glycine max) geneticamente modificadas visando maior tolerância à seca. In: CONGRESSO BRASILEIRO DE SOJA, 5.; MERCOSOJA 2009, Goiânia. Resumos... Londrina: Embrapa Soja, 2009. p.104, trab. 176. Editado por Adilson de Oliveira Júnior, Odilon Ferreira Saraiva, Clara Beatriz Hoffmann Campo, César de Castro.| Biblioteca(s): Embrapa Soja. |
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| 206. | | ROLLA, A. A. de P.; CARVALHO, J. de F. C.; FUGANTI-PAGLIARINI, R.; ENGELS, C.; RIO, A. do; MARIN, S. R. R.; OLIVEIRA, M. C. N. de; BENEVENTI, M. A.; MARCELINO-GUIMARÃES, F. C.; FARIAS, J. R. B.; NEUMAIER, N.; NAKASHIMA, K.; YAMAGUCHI-SHINOZAKI, K.; NEPOMUCENO, A. L. Phenotyping soybean plants transformed with rd29A:AtDREB1A for drought tolerance in the greenhouse and field. Transgenic Research, Dordrecht, v. 23, p. 75-87, 2014. 13 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Soja. |
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| 207. | | BARROS, L. G.; AVELINO, B. B.; SILVA, D. C. G. da; FERREIRA, E. G. C.; CASTANHO, F. M.; FERREIRA, M. E.; LOPES-CAITAR, V. S.; MARIN, S. R. R.; ARIAS, C. A. A.; LOPES, I. de O. N.; ABDELNOOR, R. V.; MARCELINO-GUIMARÃES, F. C. Mapping of a soybean rust resistance in PI 594756 at the Rpp1 locus. Molecular Breeding, v. 43, article 12, 2023. 17 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia; Embrapa Soja. |
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| 208. | | ALMEIDA, A. M. R.; PIUGA, F. F.; KITAJIMA, E. W.; GASPAR, J. O.; VALENTIN, N.; BENATO, L. C.; MARIN, S. R. R.; BINNECK, E.; OLIVEIRA, T. G. de; BELINTANI, P.; GUERZONI, R. A.; NUNES JUNIOR, J.; HOFFMANN, L.; NORA, P. S.; NEPOMUCENO, A. L.; MEYER, M. C.; ALMEIDA, L. A. Necrose da haste da soja. Londrina: Embrapa Soja, 2003. 44 p. (Embrapa Soja. Documentos, 221).| Biblioteca(s): Embrapa Soja. |
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| 209. | | HONNA, P. T.; FUGANTI-PAGLIARINI, R.; FERREIRA, L. C.; MOLINARI, M. D. C.; MARIN, S. R. R.; OLIVEIRA, M. C. N. de; FARIAS, J. R. B.; NEUMAIER, N.; MERTZ-HENNING, L. M.; KANAMORI, N.; NAKASHIMA, K.; TAKASAKI, H.; URANO, K.; SHINOZAKI, K.; YAMAGUCHI-SHINOZAKI, K.; DESIDÉRIO, J. A.; NEPOMUCENO, A. L. Molecular, physiological, and agronomical characterization, in greenhouse and in field conditions, of soybean plants genetically modified with AtGolS2 gene for drought tolerance. Molecular Breeding, v. 36, n. 11, nov. 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Soja. |
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| 210. | | BARBOSA, E. G. G.; LEITE, J. P.; MARIN, S. R. R.; MARINHO, J. P.; CARVALHO, J. de F. C.; FUGANTI-PAGLIARINI, R.; FARIAS, J. R. B.; NEUMAIER, N.; MARCELINO-GUIMARÃES, F. C.; OLIVEIRA, M. C. N. de; YAMAGUCHI-SHINOZAKI, K.; NAKASHIMA, K.; MARUYAMA, K.; KANAMORI, N.; FUJITA, Y.; YOSHIDA, T.; NEPOMUCENO, A. L. Overexpression of the ABA-dependent AREB1 transcription Factor from Arabidopsis thaliana improves soybean tolerance to water deficit. Plant Molecular Biology Reporter, v. 31, n. 3, p. 719-730, jun. 2013.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Soja. |
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| 211. | | LEITE, J. P.; BARBOSA, E. G. G.; MARIN, S. R. R.; MARINHO, J. P.; CARVALHO, J. F. C.; PAGLIARINI, R. F.; CRUZ, A. S.; OLIVEIRA, M. C. N.; FARIAS, J. R. B.; NEUMAIER, N.; GUIMARÃES, F. C. M.; YOSHIDA, T.; KANAMORI, N.; FUJITA, Y.; NAKASHIMA, K.; SHINOZAKI, K. Y.; DESIDÉRIO, J. A.; NEPOMUCENO, A. L. Overexpression of the activated form of the AtAREB1 gene (AtAREB1^QT) improves soybean responses to water deficit. Genetics and Molecular Research, v. 13, n. 3, p. 6272-6286, 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Soja. |
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| 212. | | MOLINARI, M. D. C.; FUGANTI-PAGLIARINI, R.; MARIN, S. R. R.; FERREIRA, L. C.; BARBOSA, D. de A.; MARCOLINO-GOMES, J.; OLIVEIRA, M. C. N. de; MERTZ-HENNING, L. M.; KANAMORI, N.; TAKASAKI, H.; URANO, K.; SHINOZAKI, K.; NAKASHIMA, K.; YAMAGUCHI-SHINOZAKI, K.; NEPOMUCENO, A. L. Overexpression of AtNCED3 gene improved drought tolerance in soybean in greenhouse and field conditions Genetics and Molecular Biology, v. 43, n. 3, e20190292, 2020. 12 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Soja. |
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| 213. | | MARINHO, J. P.; PAGLIARINI, R. F.; MOLINARI, M. D. C.; MARCOLINO-GOMES, J.; CARANHOTO, A. L. H.; MARIN, S. R. R.; OLIVEIRA, M. C. N. de; FOLONI, J. S. S.; MELO, C. L. P. de; KIDOKORO, S.; MIZOI, J.; KANAMORI, N.; YAMAGUCHI-SHINOZAKI, K.; NAKASHIMA, K.; NEPOMUCENO, A. L.; MERTZ-HENNING, L. M. Overexpression of full-length and partial DREB2A enhances soybean drought tolerance. AGRONOMY SCIENCE AND BIOTECHNOLOGY, v. 8, 2022. 21 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 5 |
| Biblioteca(s): Embrapa Soja. |
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| 214. | | ROLLA, A. A. P.; BENEVENTI, M. A.; FUGANTI, R.; MARTINS, M. T. B.; PEREIRA, S. S.; RUBIRA, A. P. R.; MARIN, S. R. R.; FARIAS, J. R. B.; SILVEIRA, C. A.; BINNECK, E.; ABDELNOOR, V. R.; MARCELINO, F. C.; NEPOMUCENO, A. L. Quantificação do número de cópias de inserções transgenes no genoma da soja por PCR quantitativo via quantificação absoluta e relativa. In: CONGRESSO BRASILEIRO DE GENÉTICA, 54., 2008, Salvador. Resumos... Salvador: SBG, 2008. p. 277.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 215. | | BINNECK, E.; NEPOMUCENO, A. L.; ABDELNOOR, R. V. ALMEIDA, A. M. R.; SOSA-GÓMEZ, D. R.; FARIAS, J. R. B.; BASSOI, M. C.; SILVA, J. F. V.; HOFFMANN-CAMPO, C. B.; OLIVEIRA, M. C. N.; MARCELINO, F. C.; PEREIRA, R. M.; GREGORIO, D.; MARIN, S. R. R.; SILVEIRA, C. A. Setting the bioinformatics laboratory at Embrapa Soybean aiming to ameliorate biotic and abiotic stresses. In: MEETING INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 3., 2007, São Paulo. X-Meeting 2007: proceedings. Campinas: Associação Brasileira de Bioinformática e Biologia Computacional, 2007. p. 195. 1 CD-ROM.| Tipo: Resumo em Anais de Congresso | Circulação/Nível: -- - -- |
| Biblioteca(s): Embrapa Soja. |
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| 216. | | NEPOMUCENO, A. L.; LUGLE, S.; ARIAS, C. A. A.; SILVA, J. F. V.; NEUMAIER, N.; FARIAS, J. R. B.; OYA, T.; MARIN, S. R. R.; BINNECK, E.; LEMOS, N. G.; BRETON, M. C.; MARTINS, P. K.; PEDROSO, J. C.; DELATTRE, N.; CARNEIRO, N.; LEITE, A. Transformação de plantas de soja por biobalística com genes de interesse. In: HOFFMANN-CAMPO, C. B.; SARAIVA, O. F. (Org.). Resultados de pesquisa da Embrapa Soja - 2001: ecofisiologia e biologia molecular. Londrina: Embrapa Soja, 2002. p. 40-42. (Embrapa Soja. Documentos, 198).| Biblioteca(s): Embrapa Soja. |
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| 217. | | BINNECK, E.; MORALES, A. M. R.; ALMEIDA, A. M. R.; ARIAS, C. A. A.; SILVEIRA, C. A.; SILVA, J. F. V.; FARIAS, J. R. B.; MOLINA, J. C.; PEDROSO, J. C.; BRETON, M. C.; LEMOS, N. G.; NEUMAIER, N.; MARTINS, P. K.; FUGANTI, R.; STOLF, R.; MARIN, S. R. R.; NEPOMUCENO, A. L. A visual system for DNA sequencing quality control. In: INTERNATIONAL CONFERENCE ON BIOINFOMATICS AND COMPUTATION BIOLOGY, 1., 2003, Ribeirão Preto. Resumos... [S.l.]: CBAB - Centro Brasileiro-Argentino de Biotecnologia, 2003. p. 47.| Biblioteca(s): Embrapa Soja. |
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| 218. | | 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. VSQual: a visual system to assist the DNA sequencing quality control. 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. p. 249-250. (Embrapa Soja. Documentos, 228). Editado por Flávio Moscardi, Clara Beatriz Hoffmann-Campo, Odilon Ferreira Saraiva, Paulo Roberto Galerani, Francisco Carlos Krzyzanowski, Mercedes Concordia Carrão-Panizzi.| Biblioteca(s): Embrapa Soja. |
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| Registros recuperados : 218 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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