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	Provedor de dados Nature Precedings (11) Autor James R. White (11) Malcolm Matalka (11) Samuel V. Angiuoli (11) W. Florian Fricke (10) Cesar Arze (9) The CloVR Team (9) Owen White (6) Kevin Galens (3) Michelle Gwinn Giglio (3) W. Florian Fricke (1) Mais... Palavra-chave Bioinformatics (11) Genetics & Genomics (11) Microbiology (7) Biotechnology (3) Ecology (2) Tipo do documento Manuscript (11) Ano 2011 (11) País United Kingdom (11)		Ordenar por:  Relevância Autor Título Ano Registros recuperados: 11 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 Cunningham: a BLAST Runtime Estimator Nature Precedings James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli. BLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable time frame. Waiting for BLAST to finish without having any clue of how long it’s going to take is kind of depressing, and... Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5593/version/1 Cunningham: a BLAST Runtime Estimator Nature Precedings James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli. BLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable time frame. Waiting for BLAST to finish without having any clue of how long it’s going to take is kind of depressing, and... Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5593/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/2 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; Malcolm Matalka; The CloVR Team; 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 [1] – a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates [1]; 
B) BLASTX and BLASTN [2] for functional and taxonomic assignment of sequences, respectively;
C) Metastats [3] 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... Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5886/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/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-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version1.0 Nature Precedings James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; 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 [1] – a C++ - based software package used for clustering 16SrRNA 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) naive Bayesian classifier [2] assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;
C) Qiime [3] – a python-based workflow package,... Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5888/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/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-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; 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: Biotechnology; Genetics & Genomics; Bioinformatics. Ano: 2011 URL: http://precedings.nature.com/documents/5887/version/1 Registros recuperados: 11 Primeira ... 1 ... Última

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