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greengenes: 16S rDNA data and tools
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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:
- 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.
- Graduate and postdoctoral fellowships in plant-microbe interactions at the University of Alaska with Lee Taylor
are available, read more.
- Have you registered for the International Workshop
on Ribosomal RNA Technology in Bremen, Germany (April 7-9, 2008)?
Topics include: Databases, Phylogeny, Computational Tools, PhyloChips, and Ecology. Hope to meet you there.
- 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.
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taxonomic tree of your choice and mark nodes.
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sequence records of your choice.
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Specify a
(sub-alignment) of the prokMSA to view/download.
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Calculate Consensus sequences from My Interest List (soon!).
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my local sequences/probes
against the prokMSA using or .
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the annotations of the prokMSA.
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Locate and primers within the prokMSA using pattern matching.
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a few or a few thousand 16S rDNA sequences with the NAST aligner.
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a batch of sequences using quality scores.
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alignments, taxonomies, posters, protocols, etc.
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are being developed and are available for preview.
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Infrastructure provided by:
VIMSS -
CEB -
JGI -
LBL
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