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SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.

Nucleic acids research | Dec 19, 2007

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs.

Pubmed ID: 17947321 RIS Download

Mesh terms: Base Sequence | Databases, Nucleic Acid | Genes, rRNA | Internet | Phylogeny | Quality Control | RNA, Ribosomal | Sequence Alignment | Sequence Analysis, RNA | Software

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European Molecular Biology Laboratory; Heidelberg; Germany

An international research organization that is one of the world''s top research institutions dedicated to basic research in the molecular life sciences. Outstanding training is available at multiple levels: predoctoral students, postdocs and visiting scientists are provided with exceptional training opportunities. The cornerstones of EMBL''s mission are: to perform basic research in molecular biology, to train scientists, students and visitors at all levels, to offer vital services to scientists in the member states, and to develop new instruments and methods in the life sciences, and technology transfer. Research at EMBL is conducted by approximately 85 independent groups covering the spectrum of molecular biology. The Laboratory has five units: the main Laboratory in Heidelberg, and outstations in Hinxton near Cambridge (the European Bioinformatics Institute), Grenoble, Hamburg, and Monterotondo near Rome. EMBL is international, innovative and interdisciplinary. Its 1,400 employees from 60 nations represent scientific disciplines including biology, physics, chemistry and computer science.

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Marine Ecological Genomics

A portal to georeferenced databases and tools for the analysis of marine bacterial, archaeal, and phage genomes and metagenomes. The megx.net database, MegDB (microbial ecological genomics DataBase), is a collection of publicly available georeferenced marine bacterial and archaeal genomes and metagenomes, including the Global Ocean Sampling (GOS) reads. Marine microbial genomics and metagenomics is an emerging field in environmental research. Since the completion of the first marine bacterial genome in 2003, the number of fully sequenced marine bacteria has grown rapidly. Concurrently, marine metagenomics studies are performed on a regular basis, and the resulting number of sequences is growing exponentially. To address environmentally relevant questions like organismal adaptations to oceanic provinces and regional differences in the microbial cycling of nutrients, it is necessary to couple sequence data with geographical information and supplement them with contextual information like physical, chemical and biological data. Therefore, new specialized databases are needed to organize and standardize data storage as well as centralize data access and interpretation. Megx.net is a set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts.

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