news announcement from the Ribosomal Database Project http://rdp.cme.msu.edu/misc/news.jsp Thu, 01 Sep 2005 15:00:00 EDT en-us dmcgarre@msu.edu(Donna McGarrell) RDP Release 9, Update 60 is now available. Release 9.60 contains 511,847 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#apr2208 Tues, 22 Apr 2008 18:30:00 EDT RDP Release 9, Update 59 is now available. Release 9.59 contains 489,840 aligned 16S rRNA sequences. This release includes a beta version of the new Taxomatic visualization tool. This tool displays a heatmap representation of distance matrices It helps spot errors in the underlying taxonomy. Users can scroll in all dimensions, use low zoom to examine large set, and high zoom to examine individual sequences. More Taxomatic help available. http://rdp.cme.msu.edu/misc/news.jsp#mar0508 Wed, 05 Mar 2008 11:50:00 EDT RDP Release 9, Update 58 is now available. Release 9.58 contains 481,650 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#feb0608 Wed, 06 Feb 2008 10:30:00 EDT RDP Release 9, Update 57 is now available. Release 9.57 contains 471,792 aligned 16S rRNA sequences. Release includes a new Genome Browser for viewing sequences from whole genome project. The new Genome Browser, along with Publication View, can be accessed from the Hierarchy Browser tool. http://rdp.cme.msu.edu/misc/news.jsp#jan0708 Mon, 07 Jan 2008 4:30:00 EDT RDP Release 9, Update 56 is now available. Release 9.56 contains 451,545 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#nov0807 Thu, 08 Nov 2007 11:30:00 EDT RDP Release 9, Update 55 is now available. Release 9.55 contains 440,891 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#oct1107 Thu, 11 Oct 2007 10:00:00 EDT The RDP server is experiencing an increase in the demand for alignment processing. Additional hardware has been ordered and will be put into service as soon as it is received to help speed up the processing of your sequences. http://rdp.cme.msu.edu/misc/news.jsp#sep1907 Wed, 19 Sept 2007 10:05:00 EDT RDP Release 9, Update 54 is now available. Release 9.54 contains 417,912 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#sep0407 Tue, 04 Sep 2007 16:00:00 EDT RDP Release 9, Update 53 is now available. Release 9.53 contains 409,692 aligned 16S rRNA sequences. The hierarchy model used by RDP Classifier has been updated to TOBA Release 7.7 (The Taxonomic Outline of Bacteria and Archaea), with modifications for well-defined lineages with few cultivated members, such as Acidobacteria, Verrucomicrobia and OP11. Nine taxa were removed and 305 taxa were added to the new hierarchy. About 9% of sequences were classified to greater taxonomic depth in the new release, while about 8% were classified with confidence at lesser levels. About 3.6% of sequences changed classification: 595 (0.15%) public RDP sequences changed phyla. http://rdp.cme.msu.edu/misc/news.jsp#aug0807 Wed, 08 Aug 2007 10:00:00 EDT RDP Release 9, Update 52 is now available. Release 9.52 contains 390,973 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#jul0507 Thu, 05 Jul 2007 12:30:00 EDT RDP Release 9, Update 51 is now available. Release 9.51 contains 380,520 aligned 16S rRNA sequences. It's now possible to find sequences from completed genomes by searching with the GenBank Project ID. For example, to find Aquifex aeolicus VF5 (Project ID 215), use the search term "PROID:215" in the Hierarchy Browser or directly link to url: http://rdp.cme.msu.edu/search?searchStr=PROID:215. To obtain all the sequences from the completed genomes, use the search term "genomeproject". http://rdp.cme.msu.edu/misc/news.jsp#may0207 Fri, 08 Jun 2007 9:30:00 EDT RDP Release 9, Update 50 is now available. Release 9.50 contains 368,406 aligned 16S rRNA sequences. Seqmatch results can be downloaded as a tab-delimited text file and imported into a spreadsheet program such as Excel for additional analysis. http://rdp.cme.msu.edu/misc/news.jsp#may0207 Wed, 02 May 2007 15:30:00 EDT The RDP server is experiencing an intermittent hardware problem. New parts have been ordered and the problem will not affect users' data. We regret any inconvenience. http://rdp.cme.msu.edu/misc/news.jsp#apr1107 Wed, 11 Apr 2007 10:20:00 EDT RDP Release 9, Update 49 is now available. Release 9.49 contains 351,796 aligned 16S rRNA sequences. Upgraded Tree Builder now includes bootstrap confidence estimates. http://rdp.cme.msu.edu/misc/news.jsp#apr0307 Tue, 03 Apr 2007 11:50:00 EDT New short video tutorials, demonstrating some of the more complex tasks, capture the screen with a narrator explaining the tasks and the choices available to the user Flash versions have closed captioning. http://rdp.cme.msu.edu/misc/news.jsp#mar2207 Thu, 22 Mar 2007 14:00:00 EDT RDP Release 9, Update 48 is now available. Release 9.48 contains 335,830 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#mar0107 Thu, 01 Mar 2007 11:00:00 EST RDP Release 9, Update 47 is now available. Release 9.47 contains 307,898 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#feb0107 Thu, 01 Feb 2007 16:00:00 EST RDP Release 9, Update 46 is now available. Release 9.46 contains 302,337 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#jan0907 Tue, 09 Jan 2007 15:00:00 EST RDP Release 9, Update 45 is now available. Release 9.45 contains 286,257 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#dec0606 Wed, 06 Dec 2006 16:00:00 EST RDP Release 9, Update 44 is now available. Release 9.44 contains 273,300 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#oct3106 Tue, 31 Oct 2006 16:00:00 EST RDP Release 9, Update 43 is now available. Release 9.43 contains 269,166 aligned 16S rRNA sequences. Selection on Seqmatch has been enhanced. The selection will be directly saved in Sequence Cart without routing through Hierarchy Browser. http://rdp.cme.msu.edu/misc/news.jsp#oct0606 Fri, 06 Oct 2006 18:00:00 EDT RDP site was down over weekend due to power issues. http://rdp.cme.msu.edu/misc/news.jsp#oct1606 Mon, 16 Oct 2006 12:15:00 EDT RDP Release 9, Update 42 is now available. Release 9.42 contains 262,030 aligned 16S rRNA sequences. A new analysis tool, Tree Builder to create a phylogenetic tree, is released. Some video tutorials are available to the user. Several RDP analysis services have been modified to provide extra features. When used with myRDP and/or public RDP sequences, Seqmatch reports the standard pairwise percent identity. Classifier uses the stored classification results to more rapidly display results in a taxonomic hierarchy representation.Selected RDP sequence ids (both public and myRDP) in the sequence cart can be saved and retrieved from Hierarchy Browser. An alignment mask pseudo-sequence that can be used to ‘mask out’ unalignable variable regions, and a base-pair structure pseudo-sequence are available for download from myRDP. http://rdp.cme.msu.edu/misc/news.jsp#sep1506 Fri, 15 Sep 2006 18:00:00 EDT Upload chromatograms to your myRDP pipeline is made easier than before. Now you can load raw sequencer data without defining well mapping. You can also grant research buddies permission to access your data saved in myRDP. In addtion to three existing data filters, quality filter can be applied to view only good quality sequences. Sequences were flagged as low quality using the Pintail. Read more quality test detail. http://rdp.cme.msu.edu/misc/news.jsp#aug2206 Tue, 22 Aug 2006 8:00:00 EDT RDP Release 9, Update 41 is now available. Release 9.41 contains 253,813 aligned 16S rRNA sequences. A histogram of the number of RDP sequences spanning each base position can be found on resources. http://rdp.cme.msu.edu/misc/news.jsp#jul2806 Fri, 28 Jul 2006 14:20:00 EDT RDP Release 9, Update 40 is now available. Release 9.40 contains 243,909 aligned 16S rRNA sequences. Changes with this release include unified login for myRDP and the rRNA Pipeline, the ability to update project notes and other info on myRDP, and sequences uploaded to myRDP can be viewed in the Classifier. http://rdp.cme.msu.edu/misc/news.jsp#jun3006 Fri, 30 June 2006 13:00:00 EDT Some spam filters have been rejecting the myRDP password e-mail messages. If you signed up for myRDP and haven't received your password, please contact us at rdpstaff@msu.edu and we'll e-mail your new password. p.s. We've now tuned our e-mail server and hope to avoid future problems. http://rdp.cme.msu.edu/misc/news.jsp#may3106_1 Wed, 31 May 2006 17:49:33 EDT Introduce myRDP beta release, incorporating RDP pipeline. Upload, align and classify your sequences in myRDP space. And you can organize your data, save for later analysis, add RDP sequences to your private data, and interface with standard molecular ecology tools. http://rdp.cme.msu.edu/misc/news.jsp#may1806_2 Thu, 18 May 2006 19:00:00 EDT RDP Release 9, Update 39 is now available. Release 9.39 contains 226,159 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#may1806_1 Thu, 18 May 2006 19:00:00 EDT RDP web site will be shutdown temporarily this afternoon for major software upgrade. http://rdp.cme.msu.edu/misc/news.jsp#may1806 Thu, 18 May 2006 11:20:00 EDT RDP Release 9, Update 38 is now available. Release 9.38 contains 210,976 aligned 16S rRNA sequences. The hierarchy model used by RDP Classifier has been updated to release 6.0 of Bergey's Manual of Systematic Bacteriology. The newly trained Classifier allows classification of both bacterial and archaeal 16S rRNA sequences (previous versions provided only bacterial 16S rRNA sequences classification). http://rdp.cme.msu.edu/misc/news.jsp#apr0306 Mon, 3 Apr 2006 15:00:00 EDT RDP sequences can be retrieved by uploading a file with a list of GenBank accession numbers to the RDP Hierarchy Browser. http://rdp.cme.msu.edu/misc/news.jsp#mar2306 Thu, 23 Mar 2006 3:15:00 EST RDP Release 9, Update 37 is now available. Release 9.37 contains 210,059 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#mar0206 Thu, 2 Mar 2006 11:30:00 EST RDP Release 9, Update 36 is now available. Release 9.36 contains 205,165 aligned 16S rRNA sequences. A new help page with step-by-step instructions for loading data into ARB is now available http://rdp.cme.msu.edu/misc/news.jsp#feb0206 Thu, 2 Feb 2006 13:15:00 EST RNA distance matrix in DNADist format can now be downloaded from the RDP Hierarchy Browser. Uncorrected and Jukes Cantor distance correction are the current options available. Range Queries allow one to match documents whose field(s) values are between the lower and upper bound specified by the Range Query. To find the records with accno numbers between AF068801 and AF068807 use the range search: ACC:[AF068801 TO AF068807]. Searches with different fields can be combined in one query such as ACC:[DQ179017 TO DQ179020] OR ID:[S000481300 TO S000481500]. For more information, see our Search help. http://rdp.cme.msu.edu/misc/news.jsp#jan2506 Wed, 25 Jan 2006 12:40:00 EST RDP Release 9, Update 35 is now available. Release 9.35 contains 197,833 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#jan0406 Thu, 4 Jan 2006 10:50:00 EST RDP Release 9, Update 34 is now available. Release 9.34 contains 194,696 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#dec0105 Thu, 1 Dec 2005 10:00:00 EST RDP Release 9, Update 33 is now available. Release 9.33 contains 190,785 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#nov1005 Fri, 11 Nov 2005 16:50:00 EST Genbank formatted files downloaded from the RDP between 10/7 (Friday) - 10/10 (Monday) may have corrupt publication annotation. http://rdp.cme.msu.edu/misc/news.jsp#oct1005 Mon, 10 Oct 2005 15:04:00 EDT RDP Release 9, Update 32 is now available. Release 9.32 contains 184,990 aligned 16S rRNA sequences. http://rdp.cme.msu.edu/misc/news.jsp#oct0705 Fri, 07 Oct 2005 12:50:45 EDT RDP Release 9, Update 31 is now available. Release 9.31 contains 177,880 aligned 16S rRNA sequences. Faster search and new sequence cart features. http://rdp.cme.msu.edu/misc/news.jsp#sep0605 Tue, 06 Sep 2005 15:30:30 EDT Barring any unforeseen service interruptions during MSU's Power Plant electrical generator upgrades, the RDP websites should be available through the holiday weekend. http://rdp.cme.msu.edu/misc/news.jsp#sep0105 Thu, 01 Sep 2005 14:00:00 EDT SIMO uses RDP's Sequence Match in their new RDPQuery application http://rdp.cme.msu.edu/misc/news.jsp#aug2305 Tue, 23 Aug 2005 15:00:00 EDT RDP Release 9, Update 30 is now available. Release 9.30 contains 171,253 aligned 16S rRNA sequences http://rdp.cme.msu.edu/misc/news.jsp#aug1105_2 Thu, 11 Aug 2005 08:30:30 EDT The RDP website has been moved to a faster server http://rdp.cme.msu.edu/misc/news.jsp#aug1105 Thu, 11 Aug 2005 08:00:00 EDT