Data/hora: 09/06/2024 11:50:39

Provedor de dados: 	17	
País: 	United Kingdom	
Título: 	CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.0	
Autores: 	James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.	
Data: 	2011-10-12	
Ano: 	2011	
Palavras-chave: 	Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.	
Resumo: 	The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Mothur &amp;#x2013; 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);&amp;#xd;&amp;#xa;B) The Ribosomal Database (RDP) nai&amp;#x308;ve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;&amp;#xd;&amp;#xa;C) Qiime &amp;#x2013; a python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including phylogenetic distance (UniFrac) for within-(alpha diversity) and between-(beta diversity) sample analysis;&amp;#xd;&amp;#xa;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Though some of the different protocols used in CloVR-16S overlap in purpose (e.g. OTU clustering), the end-user benefits from their overall complementary nature as they focus on different aspects of the phylogenetic analysis. CloVR-16S accepts as input raw multiplex 454-pyrosequencer output, i.e. pooled pyro-tagged sequences from multiple samples, or alternatively, pre-processed sequences from multiple samples in separate files. This protocol is available in CloVR beta versions 0.5 and 0.6.	
Tipo: 	Manuscript	
Identificador: 	http://precedings.nature.com/documents/5888/version/3

oai:nature.com:10.1038/npre.2011.5888.3

http://dx.doi.org/10.1038/npre.2011.5888.3	
Fonte: 	Nature Precedings	
Fonte: 	Creative Commons Attribution 3.0 License