
For users interested in representative (rRNA) sequence collections, the rapid growth of the data sets 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 102 data set (SILVA SSU Ref NR 102). A 99% identity criterion was applied to sort out more than 50% of the sequences within the full SSU Ref 102 (including sequences from the separated
HSM database).
Although significantly reduced in size, the SSU Ref NR is still a representative data set 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.
The All-Species Living Tree is a regularly-updated 16S 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 the third LTP release 100 from September 2009 is available. It offers 7,710 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.
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.
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
MIGS/MIMS 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 ribosomal RNA sequence data.
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 ...