Overview on our ARB/SILVA-related Projects

SSU Ref NR (non-redundant)

For users interested in representative (rRNA) sequence collections, the rapid growth of the datasets has led to immense hardware requirements paired with a significantly increased amount of time to analyse the data.

To compensate for this, the SILVA project now offers a non-redundant version of the SSU Ref dataset (SILVA SSU Ref NR). A 99% identity criterion was applied to sort out more than 50% of the sequences within the full SSU Ref.

Although significantly reduced in size, the SSU Ref NR is still a representative dataset offering a comprehensive high quality alignment and a fully classified tree reflecting the complete SILVA taxonomy, inlcuding sequences from all three domains of life. It represents the perfect starting point for your daily rRNA work based on ARB/SILVA - now again asking for just moderate hardware requirements.

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Eukaryotic Taxonomy Working Group (ETWG)

The Eukaryotic Taxonomy Working Group (ETWG) has been founded in October 2011 to create a unified taxonomy for Eukaryotes based on 18S/28S ribosomal RNA gene sequences. It is  now funded by the Gordon and Betty Moore Foundation as the UniEuk project.

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'The All-Species Living Tree' Project

 

The All-Species Living Tree is a regularly-updated 16S (SSU) rRNA-based phylogenetic tree harboring all sequenced type strains of the hitherto classified species of Archaea and Bacteria.

The project was launched in early 2008, and currently LTP release 128 as of February 2017 is available. It offers around 13,000 validated type strain sequences plus a high-quality phylogenetic tree based on an improved ARB/SILVA alignment - all within a single ARB database file, ready for download.

We also offer an 23S (LSU) rRNA-based database including 912 validated type strains.

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Contextual Data (Metadata) for Environmental Sequences

Contextual data (metadata) is the set of data describing aspects like geographic location and habitat type from which a sequence was retrieved as well as the processing of the sample.

Following the Opens external link in new windowMIGS/MIMS and MIMARKS standards for environmental samples at least providing the GPS position (longitude, latitude), depth/altitude and time of sampling is highly recommended.

The SILVA team together with the Genomics Standards Consortium has started a project to facilitate and improve the integration of contextual data for environmental sequences with an emphasis on marker genes like ribosomal RNA sequence data.

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A Standard Operating Procedure for Phylogenetic Inference (SOPPI)

A Standard Operating Procedure offering a helping hand in working through the process of contextual data acquisition, alignment, phylogenetic tree reconstruction, presentation of trees and documentation.

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International Workshop on ribosomal RNA Technology, 2008

On April 7- 9, 2008 in Bremen, Germany, in five sessions, 26 leading international speakers and about 120 participants representing diverse disciplines discussed and summarized the current status of the rRNA-based technologies. 

Thirty years have passed since Carl Woese proposed three primary domains of life based on the phylogenetic analysis of the ribosomal RNA genes. It was now the time to strategize on the best ways of proceeding on both biological and technological fronts ...

Program, Speakers, Impressions, Reports, etc.