Educators:
Jörg Peplies, Pablo Yarza, Carola Söhngen, Boyke Bunk, Frank Oliver Glöckner (Database-Node)
Date:
01-12-2015 to 04-12-2015 (9:00-17:00)
Maximum Number of Participants:
12
Location:
Max Planck Institute for Marine Microbiology Bremen
Celsiusstrasse 1
28359 Bremen
(lecture hall/PC-lab)
Contents:
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 data integration is therefore essential for microbiology, biotechnology, quality control as well as diagnostics.The SILVA ribosomal RNA databases were established in 2007 to provide high-quality reference databases of aligned rRNA gene sequences for all three domains of life. With the discontinuation of the European Ribosomal RNA Database Project, SILVA became the authoritative rDNA database project for Europe. 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, the 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 combines a theoretical and practical part. In the morning 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 largescale processing of next generation sequencing reads. In the subsequent 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
Learning goals:
Goals of the workshop are to provide the participants with the following knowledge and skills in order to prepare them for sound microbial phylogeny and diversity analysis:
- the public primary sequence databases
- concepts of marker gene sequence analysis
- concepts and usage of the secondary (rRNA gene) SILVA sequence databases
- details pf phylogenetic reconstruction (models of evolution, sequence alignments and
their evaluation, methods of tree reconstruction, evaluation of trees)
- workflows for the analysis of rRNA gene amplicon reads from NGS projects
- usage of the SILVAngs service for processing rRNA gene amplicon reads
- concepts and usage of the BacDive metadatabase
Prerequisites:
Participants should be familiar with the basic principles of molecular environmental microbiology, especially the role of the rRNA marker gene for microbial identification and phylogeny. Also, basic knowledge of Linux and elementary tools of bioinformatics (BLAST, alignment, phylogeny) is useful.
Keywords:
Microbial Diversity, 16S rRNA gene, NGS, Phylogeny, Taxonomy, Metadata, ARB, SILVA, BacDive
Tools:
- ARB (http://www.arb-home.de/)
- SILVA (http://www.arb-silva.de/)
- SILVAngs (https://www.arb-silva.de/ngs/)
- BacDive (http://bacdive.dsmz.de/)
Contact:
Jörg Peplies
+49 421 2487053
Website:
For more information see https://www.ribocon.com/training.html