Background

The SILVA databases are developed and maintained by the Opens external link in new windowMicrobial Genomics and Bioinformatics Research Group in Bremen, Germany, in cooperation with the Opens external link in new windowDepartment of Microbiology at the Technical University Munich and the company Opens external link in new windowRibocon GmbH.


SILVA is an interdisciplinary project of biologists and computer scientists to provide:

  • fully aligned and up to date small (16S/18S, SSU) and large (23S/28S, LSU) subunit  ribosomal RNA "Parc" databases on the webpage as well as ARB files
  • preconfigured subsets of only high quality, full-length sequences as ARB & FASTA files (SSU/LSU Ref)
  • extensive browse & search functionalities for sequence retrieval
  • a clear rating system for all steps of data processing with emphasis on sequence and alignment quality
  • full compatibility to the software package ARB & the latest official alignments released by the ARB project
  • compatibility to many common programs like Phylip or Paup via direct Fasta export or the ARB program
  • substantial support related to all aspects of data sets, sequence analysis and probe/primer design by our partner Opens external link in new windowRibocon GmbH.

Release information & Database history

Version 89 of our datasets have been made available in February 2007. Version 128 was released in September 2016 and increased the number of available SSU/LSU sequences to over 6,300,000. Detailed information about the content of the databases and statistics can be found  Opens internal link in current windowhere...

Motivation

Sequencing the ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction and nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA databases has been accepted by researchers worldwide as their standard tool for large scale ribosomal RNA analysis. More than 20 years of development have already been invested to extend and maintain the system. To provide high quality and comprehensive rRNA databases comprising Bacteria, Archaea and Eukarya the SILVA (from Latin silva, forest) system has been implemented in 2007. It is designed as an automatic software pipeline for sequence retrieval, quality assignment and the alignment of nucleic acid sequences based on the latest comprehensive ARB alignments.

SINA: The new SILVA (Web)Aligner

We developed a new aligner called SINA (SILVA INcremental Aligner) that is able to accurately align hundred thousands of sequences  based on a curated SEED alignment. In a first step the aligner determines the next related sequences using an optimized Suffix Tree server.  To find the optimal alignment for a new sequence up to 40 reference sequences are taken into account. While running, the system simulates the manual refinement process to optimize the result.

Features of SINA:

  • Process and quality values are added to each sequence indicating e.g. the alignment quality
  • Only minimum manual revision of the output alignment is required (e.g. no base-spreading at the ends)
  • Improved alignment quality due to advanced alignment technology compared to e.g. the ARB Aligner ("Fastaligner")

SINA is also available online for small scale projects. More information about SINA as well as the corresponding publication can be found Opens internal link in current window here.