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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 Completo
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Biblioteca(s): |
Embrapa Tabuleiros Costeiros. |
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Data corrente: |
05/02/2014 |
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Data da última atualização: |
10/03/2016 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
ARAÚJO, R. V. de; MARIA, A. N.; SANCHES, E. G.; CARNEIRO, P. C. F.; SANTOS, E. da S.; MORAIS, C. A. R. S. |
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Afiliação: |
ALEXANDRE NIZIO MARIA, CPATC; PAULO CESAR FALANGHE CARNEIRO, CPATC. |
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Título: |
Caracterização do sêmen de bijupirá (Rachycentron canadum). |
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Ano de publicação: |
2013 |
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Fonte/Imprenta: |
In: CONGRESSO BRASILEIRO DE AQUICULTURA DE ESPÉCIES NATIVAS, 4., 2013, Belém, PA. [Resumos]. [Belém, PA: s.n.], 2013. |
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Idioma: |
Português |
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Palavras-Chave: |
Bijupirá. |
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Thesagro: |
Peixe; Piscicultura. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/96917/1/Resumo-287-bijupira-semen-AN.pdf
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Marc: |
LEADER 00636nam a2200193 a 4500
001 1978654
005 2016-03-10
008 2013 bl uuuu u00u1 u #d
100 1 $aARAÚJO, R. V. de
245 $aCaracterização do sêmen de bijupirá (Rachycentron canadum).$h[electronic resource]
260 $aIn: CONGRESSO BRASILEIRO DE AQUICULTURA DE ESPÉCIES NATIVAS, 4., 2013, Belém, PA. [Resumos]. [Belém, PA: s.n.]$c2013
650 $aPeixe
650 $aPiscicultura
653 $aBijupirá
700 1 $aMARIA, A. N.
700 1 $aSANCHES, E. G.
700 1 $aCARNEIRO, P. C. F.
700 1 $aSANTOS, E. da S.
700 1 $aMORAIS, C. A. R. S.
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