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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: |
VSQual: a visual system to assist the DNA sequencing quality control. |
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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. 249-250. |
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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: |
A lack of pliant software tools that support small to medium-scale DNA sequencing efforts are a major hindrance to recording and using laboratory workflow information to monitor the overall quality of data production. To solve this task we developed a series of Perl programs that makes up a package called VSQual. This package gives rise to a Web-based graphical interface, which allows us on organizing, using and monitoring the reliability of DNA sequencing workflow data generated by automated sequencers. The package is a flexible pipeline system designed to be accessible and useful to both programmers and nonprogrammers. For each DNA sequence read, the system generates an intuitive report in FASTA colored format with visual quality information of each nucleotide position, based on Phred scores (Ewing et al., 1998, Genome Res. 8:175-85): red stands for Phred score < 10; green stands for Phred score >= 10 and < 20; blue stands for Phred score >= 20 and < 30; and, black stands for Phred score >= 30. Also, on this report, a trace viewer permits an inspection of all chromatogram extension with a graphical view of Phred score for each base. A general report for each 96-well plate is produced on a plate shape figure where the sequence quality is reported as a colored button for each well. This 96-well shape report functions as a fully clickable map, giving access to each sequence on FASTA colored format and trace viewer as described above. On the 96-well report, as default, green stands for an insert fragment of 200 or more bases with Phred score >= 20, yellow stands for a vector fragment of 200 or more bases with Phred score >= 20 if the first statement was not true, and red stands for a lower quality sequence. These parameters (Phred score and fragment size) are adjustable by the VSQual user. VSQual runs on any computer platform for which Perl is available (including Linux, Unix®, Microsoft® Windows®, and Mac® OS) and manages the data from ABI sequencer to obtain the Phred .fasta, fasta.qual and .scf, and Cross_match .fasta.screen output files which is used to build the reports on HTML format that is ready to access through any Web browser. On our lab the reports are automatically produced and placed on a local Intranet, running Apache Web server, to be used by the laboratory people. An example of the VSQual reports is disposed at http://www.cnpso.embrapa.br/bioinformatica. As our lab works based on 96-well plate shape, the scripts are designed to handle 96-well plate data but it can be customized for operate 384-well plate with few script changes. This work was supported by grants from CNPq, PRODETAB, Jircas and Embrapa. MenosA lack of pliant software tools that support small to medium-scale DNA sequencing efforts are a major hindrance to recording and using laboratory workflow information to monitor the overall quality of data production. To solve this task we developed a series of Perl programs that makes up a package called VSQual. This package gives rise to a Web-based graphical interface, which allows us on organizing, using and monitoring the reliability of DNA sequencing workflow data generated by automated sequencers. The package is a flexible pipeline system designed to be accessible and useful to both programmers and nonprogrammers. For each DNA sequence read, the system generates an intuitive report in FASTA colored format with visual quality information of each nucleotide position, based on Phred scores (Ewing et al., 1998, Genome Res. 8:175-85): red stands for Phred score < 10; green stands for Phred score >= 10 and < 20; blue stands for Phred score >= 20 and < 30; and, black stands for Phred score >= 30. Also, on this report, a trace viewer permits an inspection of all chromatogram extension with a graphical view of Phred score for each base. A general report for each 96-well plate is produced on a plate shape figure where the sequence quality is reported as a colored button for each well. This 96-well shape report functions as a fully clickable map, giving access to each sequence on FASTA colored format and trace viewer as described above. On the 96-well report, as default, green s... Mostrar Tudo |
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Categoria do assunto: |
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Marc: |
LEADER 03888naa a2200313 a 4500
001 1466824
005 2007-07-27
008 2004 bl uuuu u00u1 u #d
100 1 $aBINNECK, E.
245 $aVSQual$ba visual system to assist the DNA sequencing quality control.
260 $c2004
300 $ap. 249-250.
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 $aA lack of pliant software tools that support small to medium-scale DNA sequencing efforts are a major hindrance to recording and using laboratory workflow information to monitor the overall quality of data production. To solve this task we developed a series of Perl programs that makes up a package called VSQual. This package gives rise to a Web-based graphical interface, which allows us on organizing, using and monitoring the reliability of DNA sequencing workflow data generated by automated sequencers. The package is a flexible pipeline system designed to be accessible and useful to both programmers and nonprogrammers. For each DNA sequence read, the system generates an intuitive report in FASTA colored format with visual quality information of each nucleotide position, based on Phred scores (Ewing et al., 1998, Genome Res. 8:175-85): red stands for Phred score < 10; green stands for Phred score >= 10 and < 20; blue stands for Phred score >= 20 and < 30; and, black stands for Phred score >= 30. Also, on this report, a trace viewer permits an inspection of all chromatogram extension with a graphical view of Phred score for each base. A general report for each 96-well plate is produced on a plate shape figure where the sequence quality is reported as a colored button for each well. This 96-well shape report functions as a fully clickable map, giving access to each sequence on FASTA colored format and trace viewer as described above. On the 96-well report, as default, green stands for an insert fragment of 200 or more bases with Phred score >= 20, yellow stands for a vector fragment of 200 or more bases with Phred score >= 20 if the first statement was not true, and red stands for a lower quality sequence. These parameters (Phred score and fragment size) are adjustable by the VSQual user. VSQual runs on any computer platform for which Perl is available (including Linux, Unix®, Microsoft® Windows®, and Mac® OS) and manages the data from ABI sequencer to obtain the Phred .fasta, fasta.qual and .scf, and Cross_match .fasta.screen output files which is used to build the reports on HTML format that is ready to access through any Web browser. On our lab the reports are automatically produced and placed on a local Intranet, running Apache Web server, to be used by the laboratory people. An example of the VSQual reports is disposed at http://www.cnpso.embrapa.br/bioinformatica. As our lab works based on 96-well plate shape, the scripts are designed to handle 96-well plate data but it can be customized for operate 384-well plate with few script changes. 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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Registro |
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Registro Completo
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Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Arroz e Feijão; Embrapa Semiárido. |
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Data corrente: |
10/12/2020 |
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Data da última atualização: |
17/12/2020 |
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Tipo da produção científica: |
Capítulo em Livro Técnico-Científico |
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Autoria: |
CUADRA, S. V.; HEINEMANN, A. B.; MADARI, B. E.; ASSAD, E. D.; OLIVEIRA, P. P. A.; ANGELOTTI, F.; GIONGO, V.; VICTORIA, D. de C.; PEREIRA, L. G. R.; GONDIM, R. S.; OLIVEIRA, A. F. de; HIGA, R. C. V. |
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Afiliação: |
SANTIAGO VIANNA CUADRA, CNPTIA; ALEXANDRE BRYAN HEINEMANN, CNPAF; BEATA EMOKE MADARI, CNPAF; EDUARDO DELGADO ASSAD, CNPTIA; PATRICIA PERONDI ANCHAO OLIVEIRA, CPPSE; FRANCISLENE ANGELOTTI, CPATSA; VANDERLISE GIONGO, CPATSA; DANIEL DE CASTRO VICTORIA, CNPTIA; LUIZ GUSTAVO RIBEIRO PEREIRA, CNPGL; RUBENS SONSOL GONDIM, CNPAT; ARYEVERTON FORTES DE OLIVEIRA, CNPTIA; ROSANA CLARA VICTORIA HIGA, CNPF. |
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Título: |
Climate change and Brazilian agriculture. |
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Ano de publicação: |
2020 |
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Fonte/Imprenta: |
In: CUADRA, S. V.; HEINEMANN, A. B.; BARIONI, L. G.; MOZZER, G. B.; BERGIER, I. (Ed.). Climate action: contributions of Embrapa. Brasília, DF: Embrapa, 2020. chap. 2, p. 21-29. |
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Série: |
(Sustainable development goals, 13). |
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ISBN: |
978-65-86056-40-2 |
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Idioma: |
Inglês |
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Notas: |
Na publicação: Vanderlise Giongo Petrere. |
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Conteúdo: |
Introduction. Direct impacts. Indirect impacts. Impacts of agriculture on climate change. Conservation of ecosystem services. Public policies. Process integration as agricultural response. Final considerations. |
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Palavras-Chave: |
Agricultura brasileira; Mudanças climáticas. |
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Thesagro: |
Agricultura; Clima; Desenvolvimento Sustentável; Efeito Estufa. |
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Thesaurus NAL: |
Agriculture; Climate change; Global warming; Greenhouse gas emissions. |
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Categoria do assunto: |
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P Recursos Naturais, Ciências Ambientais e da Terra |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/219248/1/PL-Climate-action-cap2-2020.pdf
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Marc: |
LEADER 01504naa a2200409 a 4500
001 2127970
005 2020-12-17
008 2020 bl uuuu u00u1 u #d
020 $a978-65-86056-40-2
100 1 $aCUADRA, S. V.
245 $aClimate change and Brazilian agriculture.$h[electronic resource]
260 $c2020
490 $a(Sustainable development goals, 13).
500 $aNa publicação: Vanderlise Giongo Petrere.
520 $aIntroduction. Direct impacts. Indirect impacts. Impacts of agriculture on climate change. Conservation of ecosystem services. Public policies. Process integration as agricultural response. Final considerations.
650 $aAgriculture
650 $aClimate change
650 $aGlobal warming
650 $aGreenhouse gas emissions
650 $aAgricultura
650 $aClima
650 $aDesenvolvimento Sustentável
650 $aEfeito Estufa
653 $aAgricultura brasileira
653 $aMudanças climáticas
700 1 $aHEINEMANN, A. B.
700 1 $aMADARI, B. E.
700 1 $aASSAD, E. D.
700 1 $aOLIVEIRA, P. P. A.
700 1 $aANGELOTTI, F.
700 1 $aGIONGO, V.
700 1 $aVICTORIA, D. de C.
700 1 $aPEREIRA, L. G. R.
700 1 $aGONDIM, R. S.
700 1 $aOLIVEIRA, A. F. de
700 1 $aHIGA, R. C. V.
773 $tIn: CUADRA, S. V.; HEINEMANN, A. B.; BARIONI, L. G.; MOZZER, G. B.; BERGIER, I. (Ed.). Climate action: contributions of Embrapa. Brasília, DF: Embrapa, 2020. chap. 2, p. 21-29.
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Embrapa Agricultura Digital (CNPTIA) |
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