News & Events
Workshop: FISHing with tools from ARB
Speaker(s): Shi Ming Tan, phD student SCELSE
When: 03 February 2016 (3pm)
Where: SBS Classroom 3 (Level 1)
Type: Seminars

Ever since the advent of cultivation-independent molecular approaches, the ‘full-cycle rRNA approach’ has been employed as a gold standard for the study of the diversity and phylogeny of microorganisms. The full-cycle rRNA approach involves the use of the small subunit (16S rRNA) rRNA ribosomal gene as a phylogenetic molecular marker. Sequencing the 16S rRNA gene provides information that allows for the identification of microorganisms, phylogenetic analysis and design of Fluorescence in situ hybridization (FISH) probes. The exponential increase in 16S rRNA sequences has led to the development of ribosomal RNA databases: SILVA, RDP and GreenGenes.

 

The SILVA database would be briefly introduced in this talk for users who are keen on working with the 16S rRNA gene. SILVA is a secondary database that contains quality-checked and manually-curated sequences from the Bacteria, Archaea and Eukarya domain of life. Sequences contain the latest nomenclature and taxonomic classification from several providers. The perks of using SILVA as a ribosomal database would be shared. 

 

To handle the massive flood of data from the sequencing of the small subunit 16S rRNA ribosomal gene, a software package would be required to manage these data. The ARB package comprises of software tools that allow for sequence database handling and data analysis. With more than 20 years of development and system maintenance, the ARB package has been used widely by researchers for ribosomal RNA analysis. The SILVA dataset is fully compatible with the ARB software; it can be downloaded as the main dataset. Comparative sequence alignment of 16S rRNA gene sequences, construction of phylogenetic trees, taxonomic classification, probe design and matching are features offered by ARB.