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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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Classificação |
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Registro |
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Registro Completo
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Biblioteca(s): |
Embrapa Pantanal. |
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Data corrente: |
05/09/2019 |
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Data da última atualização: |
18/11/2019 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
GINJA, C.; GAMA, L. T.; CORTÉS, O.; BURRIEL, I. M.; VEGA-PLA , J. L.; PENEDO, C.; SPONENBERG, P.; CAÑÓN, J.; SANZ, A.; EGITO, A. A. do; ALVAREZ, L. A.; GIOVAMBATTISTA, G.; AGHA, S.; ROGBERG-MUÑOZ, A.; LARA, M. A. C.; DELGADO, J. V.; MARTINEZ, A.; AFONSO, S.; AGUIRRE, L.; ARMSTRONG, E.; VALLEJO, M. E. C.; CANALES, A.; CASSAMÁ, B.; CONTRERAS, G; CORDEIRO, J. M. M.; DUNNER, S.; ELBELTAGY, A.; FIORAVANTI, M. C. S.; CARPIO, M. G.; GÓMEZ, M.; HERNÁNDEZ, A.; HERNANDEZ, D.; JULIANO, R. S.; LANDI, V.; MARQUES, J. R.; MARTÍNEZ, R. D.; MARTÍNEZ, O. R.; MELUCCI, L.; FLORES, B. M.; MÚJICA, F.; PARÉS I CASANOVA, P. M.; QUIROZ, J.; RODELLAR, C.; TJON, G.; ADEBAMBO, T.; UFFO, O.; VARGAS, J. C.; VILLALOBOS, A.; ZARAGOZA, P. |
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Afiliação: |
CATARINA GINJA, UNIVERSIDADE DO PORTO; LUIS TELO GAMA, UNIVERSIDADE DE LISBOA; OSCAR CORTÉS, UNIVERSIDAD COMPLUTENSE DE MADRID; INMACULADA MARTIN BURRIEL, UNIVERSIDAD DE ZARAGOZA; JOSE LUIS VEGA-PLA, SERVICIO DE CRÍA CABALLAR DE LAS FUERZAS ARMADAS; CECILIA PENEDO, UNIVERSITY OF CALIFORNIA; PHIL SPONENBERG, VIRGINIA-MARYLAND REGIONAL COLLEGE OF VETERINARY MEDICINE; JAVIER CAÑÓN, UNIVERSIDAD COMPLUTENSE DE MADRID; ARIANNE SANZ, UNIVERSIDAD DE ZARAGOZA; ANDREA ALVES DO EGITO, CNPGC; LUZ ANGELA ALVAREZ, UNIVERSIDAD NACIONAL DE COLOMBIA; GUILLERMO GIOVAMBATTISTA, UNIVERSIDAD NACIONAL DE LA PLATA; SAIF AGHA, AIN SHAMS UNIVERSITY, CAIRO, EGYPT; ANDRÉS ROGBERG-MUÑOZ, CONICET, BUENOS AIRES, ARGENTINA.; MARIA APARECIDA CASSIANO LARA, INSTITUTO DE ZOOTECNIA; JUAN VICENTE DELGADO, UNIVERSIDAD DE CÓRDOBA; AMPARO MARTINEZ, UNIVERSIDAD DE CÓRDOBA; SÓNIA AFONSO, UNIVERSIDADE EDUARDO MONDLANE; LENIN AGUIRRE, UNIVERSIDAD NACIONAL DE LOJA; EILEEN ARMSTRONG, FACULTAD DE VETERINARIA-UDELAR; MARIA ESPERANZA CAMACHO VALLEJO, IFAPA CENTRO ALAMEDA DEL OBISPO; AMADO CANALES, UNIVERSIDAD DE CÓRDOBA; BERNARDO CASSAMÁ, DIREÇAO GERAL DA PECUÁRIA, BISSAU, GUINEA-BISSAU; GLORIA CONTRERAS, INSTITUTO NACIONAL DE INVESTIGACIONES AGRÍCOLAS - INIA; J. M. MORAS CORDEIRO, UNIVERSIDADE JOSÉ EDUARDO DOS SANTOS; SUSANA DUNNER, UNIVERSIDAD COMPLUTENSE DE MADRID; AHMED ELBELTAGY, ANIMAL PRODUCTION RESEARCH INSTITUTE; MARIA CLORINDA SOARES FIORAVANTI, UNIVERSIDADE FEDERAL DE GOIÁS; MAYRA GÓMEZ CARPIO, UNIVERSIDAD DE CÓRDOBA; MARIANO GÓMEZ, DIPUTACIÓN FORAL DE BIZKAIA; ANTONIO HERNÁNDEZ, UNIVERSIDAD VERACRUZANA; DARWIN HERNANDEZ, UNIVERSIDAD NACIONAL DE COLOMBIA; RAQUEL SOARES JULIANO, CPAP; VINCENZO LANDI, UNIVERSIDAD DE CÓRDOBA; JOSE RIBAMAR MARQUES, CPAMN; RUBÉN D. MARTÍNEZ, UNIVERSIDAD NACIONAL DE LOMAS DE ZAMORA; O. ROBERTO MARTÍNEZ, UNIVERSIDAD NACIONAL DE ASUNCIÓN; LILIA MELUCCI, UNIVERSIDAD NACIONAL DE MAR DEL PLATA; BALDOMERO MOLINA FLORES, UNIVERSIDAD DE CÓRDOBA; FERNANDO MÚJICA, UNIVERSIDAD AUSTRAL DE CHILE; PERE-MIQUEL PARÉS I CASANOVA, UNIVERSITAT DE LLEIDA; JORGE QUIROZ, INSTITUTO NACIONAL DE INVESTIGACIONES FORESTALES, AGRÍCOLAS Y PECUARIAS; CLEMENTINA RODELLAR, UNIVERSIDAD DE ZARAGOZA; GERALD TJON, MINISTRY OF AGRICULTURE, ANIMAL HUSBANDRY AND FISHERIES; TUMININU ADEBAMBO, UNIVERSITY OF AGRICULTURE ABEOKUTA; ODALYS UFFO, CENTRO NACIONAL DE SANIDAD AGROPECUARIA; JULIO CÉSAR VARGAS, UNIVERSIDAD ESTATAL AMAZÓNICA; AXEL VILLALOBOS, INSTITUTO DE INVESTIGACIÓN AGROPECUARIA; PILAR ZARAGOZA, UNIVERSIDAD DE ZARAGOZA. |
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Título: |
The genetic ancestry of american creole cattle inferred from uniparental and autosomal genetic markers. |
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Ano de publicação: |
2019 |
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Fonte/Imprenta: |
Scientific Reports, v. 9, n. 11486, p. 1-16, 2019. |
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DOI: |
10.1038/s41598-019-47636-0 |
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Idioma: |
Inglês |
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Conteúdo: |
Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development. |
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Thesagro: |
Gado; Genética Molecular; Raça. |
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Thesaurus NAL: |
Cattle breeds; Molecular genetics. |
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Categoria do assunto: |
G Melhoramento Genético |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/201658/1/The-genetic-ancestry-2019.pdf
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Marc: |
LEADER 03385naa a2200769 a 4500
001 2111963
005 2019-11-18
008 2019 bl uuuu u00u1 u #d
024 7 $a10.1038/s41598-019-47636-0$2DOI
100 1 $aGINJA, C.
245 $aThe genetic ancestry of american creole cattle inferred from uniparental and autosomal genetic markers.$h[electronic resource]
260 $c2019
520 $aCattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.
650 $aCattle breeds
650 $aMolecular genetics
650 $aGado
650 $aGenética Molecular
650 $aRaça
700 1 $aGAMA, L. T.
700 1 $aCORTÉS, O.
700 1 $aBURRIEL, I. M.
700 1 $aVEGA-PLA , J. L.
700 1 $aPENEDO, C.
700 1 $aSPONENBERG, P.
700 1 $aCAÑÓN, J.
700 1 $aSANZ, A.
700 1 $aEGITO, A. A. do
700 1 $aALVAREZ, L. A.
700 1 $aGIOVAMBATTISTA, G.
700 1 $aAGHA, S.
700 1 $aROGBERG-MUÑOZ, A.
700 1 $aLARA, M. A. C.
700 1 $aDELGADO, J. V.
700 1 $aMARTINEZ, A.
700 1 $aAFONSO, S.
700 1 $aAGUIRRE, L.
700 1 $aARMSTRONG, E.
700 1 $aVALLEJO, M. E. C.
700 1 $aCANALES, A.
700 1 $aCASSAMÁ, B.
700 1 $aCONTRERAS, G
700 1 $aCORDEIRO, J. M. M.
700 1 $aDUNNER, S.
700 1 $aELBELTAGY, A.
700 1 $aFIORAVANTI, M. C. S.
700 1 $aCARPIO, M. G.
700 1 $aGÓMEZ, M.
700 1 $aHERNÁNDEZ, A.
700 1 $aHERNANDEZ, D.
700 1 $aJULIANO, R. S.
700 1 $aLANDI, V.
700 1 $aMARQUES, J. R.
700 1 $aMARTÍNEZ, R. D.
700 1 $aMARTÍNEZ, O. R.
700 1 $aMELUCCI, L.
700 1 $aFLORES, B. M.
700 1 $aMÚJICA, F.
700 1 $aPARÉS I CASANOVA, P. M.
700 1 $aQUIROZ, J.
700 1 $aRODELLAR, C.
700 1 $aTJON, G.
700 1 $aADEBAMBO, T.
700 1 $aUFFO, O.
700 1 $aVARGAS, J. C.
700 1 $aVILLALOBOS, A.
700 1 $aZARAGOZA, P.
773 $tScientific Reports$gv. 9, n. 11486, p. 1-16, 2019.
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