de.NBI Logo

News

05.12.2015 19:05 Age: 7 yrs

Successful ARB/SILVA/BacDive training in Bremen

Many thanks to 12 fantastic international participants who made this week a memorable experience.

Analysis of the ribosomal RNA marker gene represents the gold standard for microbial identification, phylogeny, and biodiversity studies, and the sequencing efforts of this molecule have been so intense that currently the number of entries for this gene in public repositories surpasses 5 million. The understanding of the basic principles of marker gene sequence analysis and related data integration is therefore essential for microbiologists.

One of the main global resources for this marker gene is represented by the SILVA databases. They provide comprehensive collections of quality-controlled SSU and LSU rRNA gene sequences, corresponding tools (alignment, search, etc.) and are highly integrated with the ARB software package for in-depth sequence analysis and phylogenetic inference. In addition, BacDive - The Bacterial Diversity Metadatabase of the German Collection of Microorganisms and Cell Cultures offers the user a view beyond the primary sequence and its annotation by providing a comprehensive collection of organism-linked information covering the multifarious aspects of bacterial and archaeal biodiversity.

The training is split into a theoretical and practical part. In lectures, participants will get an overview on database resources and the theoretical backbone of marker gene sequence analysis, ranging from phylogenetic inference for selected organisms to the large-scale processing of next generation sequencing reads. In the practical part, the participants will get hands on experience with the SILVA databases and their tools, also including the new SILVAngs service for analysis of ribosomal RNA gene amplicon reads from next generation sequencing (NGS). The ARB software package will be used for more detailed considerations on selected sequences including manually supervised sequence alignment, phylogenetic tree reconstruction, and the evaluation of these trees. Finally, BacDive will be introduced as a tool for further data integration to better understand the biology of sequences/organisms analyzed.

This training course is organised as part of the German Network for Bioinformatics Infrastructure Opens external link in new windowde.NBI and operated by Opens external link in new windowRibocon GmbH Bremen.