With the reduced cost of sequencing, it is becoming practical to routinely survey environmental samples by single read sequencing of hundreds to thousands of rRNA clones, much like EST analysis has been used to sample expressed genes in various tissues. The Ribosomal Database Project (RDP) offers a suite of services specifically designed to accommodate this trend toward high-throughput rRNA sequencing. RDP Release 9.27 (April 2005) contains 136355 small-subunit bacterial rRNA sequences. Updated approximately monthly, these sequences are provided in aligned and annotated format and organized according to the new Bacterial Taxonomy proposed by Bergey's Manual Trust. RDP Release 9 includes a new set of user tools specifically designed for high-throughput rRNA sequence analysis. Among the tools offered in RDP Release 9, Hierarchy Browser allows users to rapidly navigate through the RDP sequence data, RDP Classifier provides a rapid taxonomic placement of one or hundreds of user sequences, RDP Library Compare finds differentially represented taxa between two rRNA libraries, the newly re-implemented Sequence Match is more accurate than BLAST at rapidly finding closely related rRNA sequences, and the new version of Probe Match finds probe and primer binding sites using a more efficient algorithm and enables users to skip partial sequences missing the target region.

The RDP-II can be found at http://rdp.cme.msu.edu/. The RDP's mission includes user support. The address for email support is rdpstaff@msu.edu. Telephone support is available at (+1 517 432 4998). The RDP-II staff may also be contacted via fax (+1 517 353 8957 Attn:RDP) or regular mail.