The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.  The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences.  If you are an ARB user, you can use greengenes to keep your own local database current.

News:

• Research Professional needed in Alaska to investigate plant-microbe interactions. visit: http://www.alaska.edu/epscor/
• Attention attendees of Metagenomics 2008 in San Diego, CA (November 3 -7). A greengenes tutorial was presented at the conference. If you have more questions, contact us.
• The Wall Street Journal picks the Berkeley PhyloChip as the top advance in environmental technology of 2008 and 3rd best innovation overall.
• Pollution Engineering Magazine selects Berkeley PhyloChip as most likely to aid pollution control and abatement in the near future.
• The Berkeley PhyloChip wins R&D100 award as one of the 100 most significant technological advances of the year.
• Dr. Mike Dyall-Smith has graciously made available his tutorial for installing Arb on the Mac OS 10.4 or 10.5 platform. Thanks Mike.
• A written summary of the International Workshop on Ribosomal RNA Technology in Bremen, Germany (April 7-9, 2008) is being prepared and should be published soon. Topics include: Databases, Phylogeny, Computational Tools, PhyloChips, and Ecology.
• We have a postdoctoral position available for a bioinformaticist to design a microarray for detection and antibiotic resistance profiling of select bacterial pathogens. Read more ...
• Thank you to all the Molecular Microbial Ecologists who joined us in discussing methods to analyze data and draw meaningful conclusions. The special session at the AGU Fall Meeting in San Francisco (December 10 - 14, 2007) helped us carve out future work to improve the analysis pipelines!
• Summer 2007 Greengenes Tutorial: The annual live tutorial for 16S rRNA gene library analysis took place on July 31st at Lawrence Berekely Lab. Please contact Jonathan Davies if you have any follow-up questions.
• Spring PhyloChip Data Analysis PowWow (April 25th, UC Berkeley) Notes: Ideas were exchanged on how to explore data generated by the G2 PhyloChip. The hot topic was how to integrate PhyloChip output with a second matrix containing treatment categories, environmental observations or patient history, as examples. Also, Jacques Ravel provided an alpha version of new software his TIGR team is developing for projecting multi-array experiments onto a phylogenetic tree. Attendees included researchers from LBL, UCB, JGI, LLNL, and Affymetrix. Contact Kristen DeAngelis if you would like to be a part of the next PowWow.
• Are you the world expert on the taxonomy of a particular phylogenetic lineage? Have you checked this database and nobody has got it right? Tell us! - we will fix it.
• We have supplemented the greengenes (Hugenholtz) taxonomy using a new automated curation tool, GRUNT (GRouping, Ungrouping, Naming Tool) developed by Daniel Dalevi. It removes most of the grunt work involved in group naming curation. Feedback welcome via this link.
• We thank Jakob Fredslund for developing a tool, Gexcellent, to convert XML trees to Newick format!
• We thank J.P. Euzéby and Hans Trüper for expert etymological advice.

Browse taxonomic tree of your choice and mark nodes.

Export sequence records of your choice.

Specify a Slice (sub-alignment) of the prokMSA to view/download.

Calculate Consensus sequences from My Interest List (soon!).

Compare my local sequences/probes against the prokMSA using BLAST or Simrank.

Search the annotations of the prokMSA.

Locate Probes and primers within the prokMSA using pattern matching.

Align a few or a few thousand 16S rDNA sequences with the NAST aligner.

Trim a batch of sequences using quality scores.

Download alignments, taxonomies, posters, protocols, etc.

More Tools are being developed and are available for preview.