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RDP-II Related Sites/Projects

FunGeneRDP's FunGene Repository provides an updated database of gene homologs based on HMM/HMMER search of the GenBank nr database and includes both protein and DNA alignments. Integrated tools are provided for primer testing, phylogenetic analysis and model refinement.

RDP's FunGene Pipeline has been developed for analyzing high-throughput gene-targeted metagenomics. The analysis methods include RDP FrameBot which detects and corrects frameshift errors while translating reads into protein sequences. These reads can then be aligned using HMMER3 aligner and clustered using RDP's mcClust complete-linkage tool which uses a memory efficient algorithm that allows clustering large numbers of unique sequences. This pipeline has been tested on several important functional genes including biphenyl dioxygenase (bphA), important for bioremediation, nitrogenase reductase (nifH), a key component in nitrogen fixation, and butyryl-CoA transferase (but) and butyrate kinase (buk), important for production of butyrate, the main energy source of human colonic epithelial cells. The FrameBot and HMM aligner were pre-configured for nifH, buk, but, alkB, bphA, cyp, dxnA, dbfA2 and carA.


probebase logoA comprehensive database containing published rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information. probeBase can be searched for target organisms or probe names and is maintained by the Microbial Ecology Group.


Primrose logo

Primrose: a program for phylogenetic probe design, is available from Kevin Ashelford at the Cardiff School of Biosciences. It uses the RDP datasets to identify phylogenetically discriminating 16S rRNA probes and primers. PRIMROSE is a stand-alone pc program and comes with a thorough tutorial.

Pintail: a tool for identifying 16S rRNA chimeras and other sequencing anomalies. The program works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene. Also includes a helpful tutorial.


JGI logo JGI's IMG: The Integrated Microbial Genomes (IMG) system provides a framework for comparative analysis of the genomes sequenced by the Joint Genome Institute. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective.


Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Consider using it in addition to the RDP's Chimera Check. Bellerophon is especially useful when you have a group of sequences likely to contain both chimeras and their parent sequences.

Bellerophon pic


Ochman's Conserved Gene Alignments: Scott Santos and Howard Ochman (University of Arizona, Tucson) have graciously made the sequence data from their paper available for distribution by the Ribosomal Database Project along with additional genes and sequences developed since publication.
Santos, S. R. and Howard Ochman. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environmental Microbiology. 2004. Jul(6)7:754-9. [PubMed 15186354]
View sequence downloads on our Resources page


Other Michigan State University Sites:

Center for Microbial Ecology logo
The Center for Microbial Ecology
at Michigan State University
MMG logo
MSU's MMG Department
rrndb logo
Ribosomal RNA Operon
Copy Number Database



Questions/comments: rdpstaff@msu.edu
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