Home Itens selecionados Provedores de dados OAI Créditos Sobre Ajuda

			Busca avançada
	Provedor de dados Nature Precedings (10) Autor Owen White (10) Cesar Arze (8) James R. White (8) Samuel V. Angiuoli (8) The CloVR Team (8) W. Florian Fricke (8) Malcolm Matalka (6) Michelle Gwinn Giglio (4) Andreas Wilke (2) Anjanette Johnston (2) Antonio Gonzalez (2) Aymé Spor (2) Barbara A. Methé (2) Bruce W. Birren (2) Catherine A. Lozupone (2) Christian L. Lauber (2) Christopher Hunter (2) Dan Knights (2) David A. Relman (2) Dawn Field (2) Mais... Palavra-chave Bioinformatics (10) Genetics & Genomics (10) Microbiology (10) Ecology (4) Biotechnology (2) Earth & Environment (2) Data Standards (1) Mais... Tipo do documento Manuscript (10) Ano 2011 (8) 2010 (2) País United Kingdom (10)		Ordenar por:  Relevância Autor Título Ano Registros recuperados: 10 Primeira ... 1 ... Última CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0 Nature Precedings Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke. The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or... Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5887/version/2 The “Minimum Information about an ENvironmental Sequence” (MIENS) specification Nature Precedings Pelin Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R. Cole; Linda Amaral-Zettler; Jack A. Gilbert; Ilene Karsch-Mizrachi; Anjanette Johnston; Guy Cochrane; Robert Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Phillipe Rocca-Serra; Peter Sterk; Mani Arumugam; Laura Baumgartner; Bruce W. Birren; Martin J. Blaser; Vivien Bonazzi; Peer Bork; Pier Luigi Buttigieg; Patrick Chain; Elizabeth K. Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed Fuhrman; Rachel E. Gallery; Richard A. Gibbs; Michelle Gwinn Giglio; Inigo San Gil; Elizabeth M. Glass; Antonio Gonzalez; Jeffrey I. Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L. Lauber; Teresa Legg; Ruth E. Ley; Catherine A. Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn Maguire; Barbara A. Methé; Folker Meyer; Sara Nakielny; Karen E. Nelson; Diana Nemergut; Josh D. Neufeld; Norman R. Pace; Giriprakash Palanisamy; Jörg Peplies; Jane Peterson; Joseph Petrosino; Lita Proctor; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A. Relman; Susanna Assunta-Sansone; Lynn Schriml; Erica Sodergren; Aymé Spor; Jesse Stombaugh; James M. Tiedje; Doyle V. Ward; George M. Weinstock; Doug Wendel; Owen White; Andreas Wilke; Jennifer Wortmann; Frank Oliver Glöckner. We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere. Tipo: Manuscript Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics; Earth & Environment. Ano: 2010 URL: http://precedings.nature.com/documents/5252/version/1 CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.1 Nature Precedings James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke. The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets: 

A) Qiime – a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier; 
B) UCHIME – a tool for rapid identification of chimeric 16S sequence fragments; 
C) Mothur – a C++-based software package for 16S analysis;
D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.
 
CloVR-16S... Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/6287/version/2 The “Minimum Information about an ENvironmental Sequence” (MIENS) specification Nature Precedings Pelin Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R. Cole; Linda Amaral-Zettler; Jack A. Gilbert; Ilene Karsch-Mizrachi; Anjanette Johnston; Guy Cochrane; Robert Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Phillipe Rocca-Serra; Peter Sterk; Mani Arumugam; Laura Baumgartner; Bruce W. Birren; Martin J. Blaser; Vivien Bonazzi; Peer Bork; Pier Luigi Buttigieg; Patrick Chain; Elizabeth K. Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed Fuhrman; Rachel E. Gallery; Richard A. Gibbs; Michelle Gwinn Giglio; Inigo San Gil; Elizabeth M. Glass; Antonio Gonzalez; Jeffrey I. Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L. Lauber; Teresa Legg; Ruth E. Ley; Catherine A. Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn Maguire; Barbara A. Methé; Folker Meyer; Sara Nakielny; Karen E. Nelson; Diana Nemergut; Josh D. Neufeld; Norman R. Pace; Giriprakash Palanisamy; Jörg Peplies; Jane Peterson; Joseph Petrosino; Lita Proctor; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A. Relman; Susanna Assunta-Sansone; Lynn Schriml; Erica Sodergren; Aymé Spor; Jesse Stombaugh; James M. Tiedje; Doyle V. Ward; George M. Weinstock; Doug Wendel; Owen White; Andreas Wilke; Jennifer Wortmann; Frank Oliver Glöckner. We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere. Tipo: Manuscript Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics; Earth & Environment; Data Standards. Ano: 2010 URL: http://precedings.nature.com/documents/5252/version/2 CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.1 Nature Precedings James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke. The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets: 

A) Qiime – a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier; 
B) UCHIME – a tool for rapid identification of chimeric 16S sequence fragments; 
C) Mothur – a C++-based software package for 16S analysis;
D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.
 
CloVR-16S... Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/6287/version/1 CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.0 Nature Precedings James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke. The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:

A) Mothur – a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);
B) The Ribosomal Database (RDP) naïve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;
C) Qiime – a python-based workflow package,... Tipo: Manuscript Palavras-chave: Ecology; Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5888/version/3 CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0 Nature Precedings James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke. The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:

A) UCLUST – a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates;
B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively;
C) Metastats and custom R scripts to generate additional statistical and graphical evaluation.

The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples,... Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5886/version/2 CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.0 Nature Precedings James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke. The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:

A) Mothur – a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);
B) The Ribosomal Database (RDP) naïve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;
C) Qiime – a python-based workflow package,... Tipo: Manuscript Palavras-chave: Ecology; Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5888/version/2 CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0 Nature Precedings Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke. The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or... Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5887/version/3 CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0 Nature Precedings James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke. The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:

A) UCLUST – a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates;
B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively;
C) Metastats and custom R scripts to generate additional statistical and graphical evaluation.

The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples,... Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5886/version/3 Registros recuperados: 10 Primeira ... 1 ... Última

Empresa Brasileira de Pesquisa Agropecuária - Embrapa Todos os direitos reservados, conforme Lei n° 9.610 Política de Privacidade Área restrita		Embrapa Parque Estação Biológica - PqEB s/n° Brasília, DF - Brasil - CEP 70770-901 Fone: (61) 3448-4433 - Fax: (61) 3448-4890 / 3448-4891 SAC: https://www.embrapa.br/fale-conosco