RDP-II Related Sites/Projects
A
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.
http://www.microbial-ecology.net/probebase/
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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'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.
http://img.jgi.doe.gov/
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. |
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An original data analysis tool for visualizing the taxonomic relationships
among the prokaryotes. The relationships are based on the evolutionary
distances between the organisms, as measured using the small subunit ribosomal
RNA (SSU rRNA) molecule.
http://taxoweb.mmg.msu.edu/
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:
 The Center for Microbial Ecology at Michigan State University |
 MSU's MMG Department |
 Ribosomal RNA Operon Copy Number Database |
Questions/comments: rdpstaff@msu.edu
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