New publications on ribosomal RNA tools (databases, software, etc)

For those doing microbial diversity studies, analysis of rRNA genes via PCR is still a fundamental tool.  And thankfully many people keep maintaining various databases and tools for people to use to carry out analysis of rRNA data.  Here are some new papers of relevance:

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.

Ribosomal Database Project: data and tools for high throughput rRNA analysis

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names

Infernal 1.1: 100-fold faster RNA homology searches

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies

Data Analysis

Leave a Reply

Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.