| summaries | full news articles |
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This site will be shutdown soon.
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01/1/2008, 02:41 pm
The RDP 8.1 (this site) is scheduled to be taken offline in 6 months time (June, 2008). It may disappear sooner, however, should an unexpected hardware or software error occur. If you have concerns or requests about this site's closure, please contact the RDP Staff. Most of the functionality from RDP8.1 is available in the latest RDP releases. If this site meets a need the latest release does not, please contact us and we may be able to help you. RDP 8.1 was replaced by the latest RDP release (RDP 9) over 3 years ago. This site has been left online as-is as a convenience to our users who did not wish to immediately switch to the latest tools and data. |
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RDP Release 9 is now available. RDP 8.1 (this site) is no longer being maintained.
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09/15/2004, 09:26 am
RDP Release 9 is now available. RDP 9 contains over 100,000 sequences and is updated monthly. More info on RDP 9 can be found in the release notes. RDP 8.1 tools and data have been moved to a new URL (http://rdp8.cme.msu.edu). RDP 8.1 will continue to be available for an indefinite period as a convenience to our users, but is no longer being maintained by the RDP. For the latest news, data, and analysis tools please use Release 9. |
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Conserved Gene Alignments Available
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08/04/2004, 05:26 pm
The conserved gene and protein alignments from the recent paper "Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins" [Santos, S.R. & H. Ochman (2004) Environmental Microbiology 7:754-759] have been provided to the RDP by Howard Ochman. Each alignment can be downloaded in both fasta and nexus formats here. |
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The RDP is pleased to announce a related MSU project: The Taxonomy Browser™
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06/08/2004, 03:18 pm
From the website:  ™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. |
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RDP's poster from ASM 2004 is now available.
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06/02/2004, 11:36 am
RDP's poster displayed at ASM 2004 is available on the downloads page. |
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New and updated Preview Release tools available. New RDP Classifier and updated Hierarchy Browser.
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05/22/2004, 02:22 pm
Two new tools are available for the Preview Release: Hierarchy Browser The Hierarchy Browser has been completely redone with a faster and better looking interface. Browsing, selecting, and downloading sequences should be significantly easier and faster with the new version. RDP Classifier This is the first public release of the RDP Classifier, a tool for initial assignment of your sequences to Bergey's Taxonomy. We have been using this classifier internally to place sequences from our Preview Release into the Hierarchy Browser. |
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Server Upgrade
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05/21/2004, 11:12 am
The RDP has moved to a new and faster server. Some sequence lists and phylip sessions created Friday afternoon (5/21/2004) may not be available. If you experience any dead links or problems running programs, please let us know. |
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April update of the Preview Release out.
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05/05/2004, 01:46 pm
The April update of the Preview Release contains an additional 1,231 sequences, bringing the total to 97,128 16s rRNA sequences. Please see this announcement for further information about this release. |
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March update of the preview release out.
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03/29/2004, 04:38 pm
The March update of the Preview Release contains an additional 3,084 sequences, bringing the total to 95,897 16s rRNA sequences. Please see this announcement for further information about this release. |
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February update of the preview release out.
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03/02/2004, 04:16 pm
The February update of the Preview Release contains an additional 4,953 sequences, bringing the total to 92,813 16s rRNA sequences. With this release, the Sequence Match program has reached a limit on the number of sequences it can search. Consequently, the dataset Sequence Match searches does not include recently added sequences. Sequence Match will be updated soon to allow for larger RDP databases, run faster, and have an improved interface. |
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January update of the preview release out.
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02/06/2004, 12:28 pm
1,791 new sequences have been added to the RDP Preview Release. The Preview Release now contains 87,860 aligned 16s rRNA sequences. |
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December update of the preview release out.
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01/07/2004, 10:53 am
2,109 new sequences have been added to the RDP Preview Release. The Preview Release now contains 86,069 aligned 16s rRNA sequences. |
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November update of the preview release out.
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12/05/2003, 04:57 pm
A little later then usual, but... 4,057 new sequences have been added to the RDP Preview Release. The Preview Release now contains 83,960 aligned 16s rRNA sequences. In addition, sequences in the RDP Hierarchy have been reclassified using release 4.0 of the Taxonomic Outline of the Prokaryotes from Bergey's Manual of Systematic Bacteriology. |
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October update of the preview release out.
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10/29/2003, 11:59 pm
1,688 new sequences have been added to the RDP Preview Release. The Preview Release now contains 79,903 aligned 16s rRNA sequences. |
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September update of the preview release out.
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10/06/2003, 03:33 pm
1,849 new sequences have been added to the RDP Preview Release. The Preview Release now contains 78,215 aligned 16s rRNA sequences. |
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August update of the preview release out.
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08/29/2003, 05:37 pm
2,256 new sequences have been added to the RDP Preview Release. The Preview Release now contains 76,366 aligned 16s rRNA sequences. |
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July update of the preview release out.
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07/25/2003, 02:48 pm
1,484 new sequences have been added to the RDP Preview Release. The Preview Release now contains 74,110 aligned 16s rRNA sequences. |
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June update of the preview release out.
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06/25/2003, 05:33 pm
1,535 new sequences have been added to the RDP Preview Release. The Preview Release now contains 72,626 aligned 16s rRNA sequences. |
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May update of the preview release out.
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05/30/2003, 08:12 pm
1,888 new sequences have been added to the RDP Preview Release. The Preview Release now contains 71,091 aligned 16s rRNA sequences. |
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RDP's poster from ASM 2003 is now available.
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05/26/2003, 05:12 pm
RDP's poster displayed at ASM 2003 is now available on the downloads page. |
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April update of the Preview Release out.
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04/18/2003, 05:33 pm
3,331 new sequences have been added to the RDP Preview Release. The Preview Release now contains 69,203 aligned 16s rRNA sequences. Also with this update, 51 sequences identified as chimeric by Hugenholtz and Huber have been moved into the hierarchy node labeled Putative Chimera (level 1.31 in the RDP Hierarchy, level 1.3.3 on the RDP's version of NCBI's Hierarchy). |
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Website email functions fixed.
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04/08/2003, 04:14 pm
UPDATE 6pm EST April 8: This issue has been fixed. Issues with the RDP server are causing all email sent from the server (emailed analysis results, user support and feedback forms) to be lost. All email sent since 2pm EST April 8, 2003 has been lost. We are currently working to fix this problem. Email sent to rdpstaff@msu.edu from your normal email program (ms outlook, eudora, etc) is not effected. |
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New Chimera detection program, Bellerophon, released by Phil Hugenholtz and Thomas Huber.
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04/03/2003, 11:32 am
Phil Hugenholtz and Thomas Huber have released a new chimera detection program, Bellerophon, which is available at http://foo.maths.uq.edu.au/~huber/bellerophon.pl. 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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March update of the Preview Release out.
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03/20/2003, 04:08 pm
1,175 new sequences have been added to the RDP Preview Release. The Preview Release now contains 65,872 aligned 16s rRNA sequences. Additionally, the Preview Release alignment is now available as a seperate download. |
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Febuary update of the Preview Release out.
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02/19/2003, 05:10 pm
1,935 new sequences have been added to the RDP Preview Release. The Preview Release now contains 64,697 aligned 16s rRNA sequences. In addition, Sequence Descriptions have been changed to match names given in DSMZ's Bacterial Nomenclature Up-to-date where available. |
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January update of the Preview Release out.
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01/24/2003, 04:27 pm
2,488 new sequences have been added to the RDP Preview Release. The Preview Release now contains 62,762 aligned 16s rRNA sequences. |
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December update of the Preview Release out.
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12/19/2002, 06:36 pm
2,501 additional sequences have been added to the RDP Preview Release for a total of 60,274 16S rRNA sequences. In addition, the preview RDP Hierarchy has been changed to reflect a recent update of Bergey's Taxonomy. |
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More sequences added to the Preview Release
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11/21/2002, 12:47 pm
The RDP Preview Release has been updated with 5,888 additional sequences. The Preview Release now has 57,773 16S rRNA sequences for use with two analysis tools. |
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Mirror site temporarily down.
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11/08/2002, 03:44 pm
The Japanese Mirror site is currently offline. We are unsure when it will be back online. |
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Preview Release updated.
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10/29/2002, 03:10 pm
The RDP Preview Release has been updated with 1,830 additional sequences. The release now contains 51,885 16S rRNA sequences. In addition, the Hierarchy Browser Preview's search capabilities have been updated, and all Preview Release analysis tools have received cosmetic updates. |
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Phylip Interface updated to include the weighbor treeing method.
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09/13/2002, 06:29 pm
The RDP's Phylip Interface has been updated. The UPGMA treeing method has been replaced with the Weighted Neighbor Joining (weighbor) method. |
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Protocol for improved T-RFLP by capillary electrophoresis available.
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08/08/2002, 03:30 pm
A protocol for improved T-RFLP by capillary electrophoresis, which includes a sample, PCR protocol information, references and suggested readings, is now available. From V. Grüntzig, B. Stres, H. L. Ayala del Río, and J. M. Tiedje of MSU's Center for Microbial Ecology. |
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Recent website issues fixed.
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07/17/2002, 01:01 pm
The RDP recently experienced a disk problem that caused some tools to fail when users uploaded data. This problem has been fixed. |
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PRIMROSE, a program for phylogenetic probe design, is now available!
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07/09/2002, 09:43 am
PRIMROSE,a new 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. Many of our users have asked for probe design help. Please let us know if PRIMROSE meets your needs. |
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Hugenholtz alignment now available.
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02/18/2002, 12:39 pm
The RDP thanks Dr. Philip Hugenholtz for making his Combined Alignment available for RDP users. The Combined Alignment includes 35 bacterial and 18 archaeal phylum-level lineages and is now available in ARB format in the RDP's download section. The alignment is further described in the accompanying release notes. |
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Mirror site temporarily unavailable.
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01/16/2002, 10:23 am
The Japanese mirror site will be unavailable for the weekend starting the 18th of January. (01/21/2002 The mirror site is once again available -rdp staff) |
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Japanese mirror site online.
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11/19/2001, 02:36 pm
The link to the Japanese Mirror Site can be found on our homepage. If our present website is experiencing heavy traffic, we encourage our users to visit our mirrror site. |
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Analysis tools updates.
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08/23/2001, 12:10 pm
RDP-II has made updates in Sequence Aligner, Sequence Match, and TAP-TRFLP tools in the Online Analyses section. Sequence Aligner has several cosmetic fixes in the HTML alignment display. In Sequence Match, the "Expand the RDP with your own sequences" option broke during our recent move to our new server, so we have been forced to temporarily remove this option while we track down the problem. In TAP-TRFLP we have fixed a bug that may have caused incorrect results with reverse primers. We encourage our users to re-check all previous TAP-TRFLP reverse primer analyses. |
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The Phylip Interface program has been updated.
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07/03/2001, 12:48 pm
The Phylip Interface program has been updated to allow re-rooting at any position along any horizontal branch of a tree. |
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Release 8.1 Poster presented at ASM now available.
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06/01/2001, 03:26 pm
Release 8.1 Poster presented at ASM now available online! The 2001 Poster can be found at http://rdp8.cme.msu.edu/pubs/NAR/ASM2001poster.pdf. |
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The RDP-II Release 8.1 is online.
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05/18/2001, 04:30 pm
The Ribosomal Database Project II proudly announces Release 8.1 of its web site and data. The number of Eukaryotic sequences has increased from 2,054 to 5,186. In addition, 85 new trees are available for download, each spanning a subset of Prokaryotic diversity. This release also introduces two new web tools. The first new tool, Hierarchy Browser, allows searching and has visual indicators of sequence length and quality. The second, the Phylip interface, allows the user to create distance, or similarity, matrices and phylogenetic trees using any combination of personal sequences and sequences from the RDP. The final enhancement to the RDP for this release is an online tutorial for the Chimera Check, Sequence Aligner, Sequence Match, and Similarity Matrix analysis tools. Tutorial modules for the other RDP web tools will be available in the near future. |
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SSU_Prok.arb file has been updated with a new tree.
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09/01/2000, 11:30 am
The ARB file for the SSU Prokaryotes now includes a tree that will allow you to navigate all 16,277 sequences. If you've already downloaded and made modifications to the original ARB file, you may obtain the new one and export the new tree for use with your modified ARB file. |
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Changes have been made to the ARB data file and tree files for Release 8.0.
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06/30/2000, 03:07 pm
The following updates have been made to Release 8.0 phylogenetic trees (available June 1, 2000):
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Tree Viewer has been updated with Release 8.0 trees.
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06/15/2000, 08:44 am
The Release 8.0 newick trees are now available for viewing with the treeview program. |
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Release 8.0 is now available on the RDP FTP site. [FTP NO LONGER AVAILABLE]
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06/07/2000, 03:08 pm
The RDP-II ftp site now contains data for Release 8.0 including the new trees for selected sequences. See the README and TREEFILE_HIERARCHY files in the release 8 tree directory for more information. |
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The web site has been updated.
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06/01/2000, 05:53 pm
The web site has been updated with the Release 8.0 data. The data will also be available on the ftp site soon. |
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Please read our new License Agreement.
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06/01/2000, 04:50 pm
Before using the Online Analyses or downloading the RDP Release 8.0 data, please take a moment to read the new RDP License Agreement. |
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Release 8.0 is now available!
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06/01/2000, 05:28 pm
Release 8.0 from the Ribosomal Database Project II is now available with 16,277 aligned SSU prokaryotic sequences and 30,322 unaligned SSU sequences. Also, a new backbone tree of 218 SSU prokaryotic sequences (and other smaller grouped trees) will be available soon for downloading at pub/RDP/SSU_rRNA/trees/release_8.0_trees. |
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Unexpected interruption in service.
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12/28/1999, 07:44 pm
We apologize for the inconvenience that the unexpected network outage from 1999.12.23 - 1999.12.27 caused for our users. The outage was not related to year 2000 problems, in case anyone is wondering. We expect our site to be fully operational through the new year. Thank you all for your continuing interest in the Ribosomal Database Project. |
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Planned network outage.
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10/28/1999, 01:38 pm
Network service to the Ribosomal Database Project and other sites at Michigan State University will be unavailable from 5:30am to 7:00am on Friday, October 29. |
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Probe Match update.
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10/18/1999, 01:02 pm
A minor correction has been made to the results from the Probe Match program. The output had incorrectly labeled the probe and target sequences, which has caused some confusion when interpreting the results. The labels are now correct. The actual results from the program were unaffected by this problem. |
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Prokaryotes available in ARB format.
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10/08/1999, 05:05 pm
The RDP is now providing the release 7.1 data in an ARB-formatted file, available on the ftp server (no longer available). Currently, only the Prokaryotes are available in this format (which has been compressed with gzip), but the other data sets will be available within a week or so. Newick trees for the Prokaryotic, Eukaryotic and Mitochondrial alignments (with RDP short ID's for ARB) are all available, as of October 11th. |
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More fixes performed.
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10/07/1999, 03:27 pm
Access to the ftp site via HTTP (http://ftp.cme.msu.edu/pub/RDP/) has not been working for a few days. We've fixed the problem. This did not affect access via normal ftp clients, or web browsers using the FTP protocol (ftp://ftp.cme.msu.edu/pub/RDP/). FTP IS NO LONGER AVAILABLE -- all our files can be found through the download area. Also, some links in the online documentation have been corrected. |
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Some fixes.
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10/05/1999, 04:13 pm
The "Mail Results" option was broken for several of the analysis programs over the weekend. This has been fixed, and should be working properly now. If you encounter any problems at all with the site, please let us know and we will deal with them as quickly as possible. |
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Web site updates.
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09/24/1999, 05:57 pm
Some updates have been made to the RDP web site in order to facilitate user feedback and more readily supply information to our user community. A new support mail program is in place which is linked at the bottom of most pages on this site, and will direct mail to the appropriate RDP staff member(s). We have updated the documentation for our online analyses, and have created a Frequently Asked Questions (FAQ) for each program. A new announcement system is in place, which provides the latest news about the RDP. |
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Mirror site planned for Japan.
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09/17/1999, 06:40 pm
We are happy to announce plans for an RDP mirror site in Japan. The mirror site is being developed in cooperation with the Laboratory for Molecular Classification in the Center for Information Biology at the National Institute of Genetics (NIG), Japan. This new mirror site should provide better access to RDP-II for researchers in that part of the world. |
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RDP-II Release 7.1 is available.
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09/17/1999, 05:00 pm
Release 7.1 is here. It adds 1117 new sequences, over 850 are sequences from prokaryotic type strains. A special effort has been made to identify sequences from type material throughout the SSU prokaryotic datafile. The balance of the new sequences were chosen to represent more of the breadth of prokaryotic diversity. We have a new TAP T-RFLP analysis program, other analysis programs have been overhauled and support files have been greatly enhanced. Also, the URL for the RDP mainpage has changed slightly; make sure you update your bookmarks. |
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Analyses have been updated.
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09/17/1999, 04:35 pm
Some changes have been made to the analysis programs, based on user requests. The file upload procedure has been modified to better handle your data during the upload process. Error messages have been rewritten to be more useful. Some slight cosmetic changes have also been made to the program output. |
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A new RDP sequence selection tool is available.
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03/03/1999, 03:52 pm
A pre-release version of our new RDP Sequence Selection Tool is now available from the Analysis page. This location may change eventually. Since this is a pre-release, expect some of the functionality to change as we make improvements. Please look at the online documentation for more information. If you have any comments or questions about it, please send mail to RDP-II Information Systems Team. |
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The citation for RDP is now available for the 2000 NAR article.
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06/01/2000, 09:22 am
The RDP-II citation has been updated for the 2000 NAR article. |
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A process monitor is available for our server.
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11/24/1998, 08:46 pm
A process monitoring program is now available. If you are experiencing problems with the analysis programs, you may want to check there first to find out if the server is overloaded. If this is the case, please let us know, as it is usually due to a runaway process. |
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New interfaces for Online Analyses!
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08/27/1998, 12:14 pm
The interfaces for the Check Probe, Sequence Match, Sequence Align, Chimera Check, and Alignment Slices have been updated. The old problem of incompatibilities with other web browsers has been resolved. File uploads now work with Netscape and Internet Explorer on all platforms. Also, Cut & Paste boxes are available for sequence entry on many of the analysis programs. Try it out, and let us know how it works! The remaining analysis programs are currently in the process of being updated and will be online as soon as they are available. |
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A UIUC to MSU migration guide is online.
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07/21/1998, 01:35 pm
If you're familiar with the old website, the online migration guide (no longer available) can help you with the switch to our new site. Confused about how the new analysis functions compare to the functions at the old website? The answers are in the migration guide! |
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The UIUC site is still available.
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07/21/1998, 01:42 pm
The former RDP website is still available at http://www.life.uiuc.edu. Both sites contain the same release 7.0 data, but offer slightly different analysis functions. This will probably be the last data update for the old website. |
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