Dear RDP and ARB user

Here is a recent update (1/02) of my 16S rDNA ARB database compiled in the 
excellent ARB software package (http://www.arb-home.de/) and based on the 
original March 1997 release. I just want to say that if you're not using ARB to 
make your trees, you should be!

Some specifics:

i) This database is heavily biased towards prokaryotes, particularly novel 
phyla, with only about 100 eukaryal sequences included to use as 
outgroups.

ii) I continue to use the old 6000 character ARB alignment (1997 release) 
rather than the new 26,000 character alignment (2001 release) because the 
smaller alignment runs much faster on your average computer. Most of the 
increases in alignment length seem to be have been added to 
accommodate eukaryal sequences and in the limited instances where a 
prokaryotic sequence doesn't fit into the 6000 character alignment, I've 
removed the offending stretch of sequence and flagged the deletion in the 
"warning" field.

iii) Needless to say, this database does not have all the 16S rDNA sequences 
available in the public databases. This is an impossible task for one person 
and I have favoured adding near complete sequences (>1300 nt) over 
partial sequences.

iv) As far as possible, I've labelled groups according to the new Bergey's 
Manual of Systematic Bacteriology Taxonomic Outline available at 
http://www.cme.msu.edu/bergeys/. I really like this effort to standardise 
prokaryote taxonomy, despite it's adoption of the term phylum over division. 
Bergey's doesn't tackle environmental candidate phyla (divisions), however, 
and the naming of these is usually based on the first clone sequences 
released to the databases in the group, or using published group names if 
they exist. If a cultivated representative pops up, I rename the group to the 
cultivar e.g. Gemmimonas, formally known as the BD or KS-B group.

v) Many but not all variable regions have been aligned by hand.

vi) Beware sequences ending with a "#". These have been identified as 
chimeric by partial treeing analysis. Specifics about the chimera are given in 
the "warning" field (see associated ref below).

If I have missed important (preferably full length) sequences, or mucked up an 
alignment, or if you don't agree with the groupings or naming scheme, please 
don't hesitate to contact me. My intention is to make regular ARB database 
updates available at this site.

BW, Phil Hugenholtz
19 Jan 2002

ComBinE group, Advanced Computational Modelling Centre, The University of 
Queensland, Brisbane 4072, Australia.
Email: philiph@biosci.uq.edu.au (will be active for a few more months)

New address, as of 9 February 2002, will be the Department of Environmental 
Science, Policy and Management, Hilgard Hall, University of California Berkeley, 
Berkeley CA 94720, USA.
Probable email: philiph@nature.berkeley.edu


Associated References:

Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome 
Biology. In press.

Hugenholtz, P. Chimeric 16S rDNA sequences of diverse ancestry are 
accumulating in the public databases. Submitted to AEM 15/1/02.