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3D rRNA modification maps

http://people.biochem.umass.edu/fournierlab/3dmodmap/

Description :
Locations of modified rRNA nucleotides within the 3D structure of the ribosome

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data

http://www.arb-silva.de/

Description :
Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. To cope with the deluge of data, the SILVA system (from Latin silva, forest) was implemented to provide a central, comprehensive web resource for up to date, quality controlled databases of aligned small- and large subunit rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies and carry a rich set of process information. An intuitive ranking system allows the user to get a rapid overview about the quality of the sequences. SILVA is designed as a central comprehensive resource by integrating multiple taxonomic classifications and the latest validly described nomenclature as well as additional information, such as if a sequence was derived from a cultivated organism, a type strain, or belongs to a genome project. All databases are fully compatible with the widely used ARB software package for phylogenetic inference and probe design.

Aknowledgement :
We would like to thank Ralf Westram for expert assistance with the ARB software suite. We would also thank James Cole and the RDP II team for help with Pintail and fruitful discussions. We are grateful for funding from the Max Planck Society.

References :
Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W.G., Peplies, J. and Glöckner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acid Res., 35, 7188-7196.

NAST

http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi

Description :
Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.

Ribosomal Database Project

http://rdp.cme.msu.edu/

Description :
Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download.

16S and 23S Ribosomal RNA Mutation Database

http://ribosome.fandm.edu/

Description :
Access to the expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases has been improved to permit searches of the lists of alterations for all the data from (1) one specific organism, (2) one specific nucleotide position, (3) one specific phenotype, or (4) a particular author. The URL for the searchable version of the Databases is: http://ribosome.fandm.edu. The database currently consists of 1024 records, including 485 16S rRNA records from Escherichia coli, 37 16S-like rRNA records from other organisms, 421 23S rRNA records from E. coli, and 81 23S-like records from other organisms. The numbering of positions in all records corresponds to the numbering in E. coli. We welcome any suggested revisions to the database, as well as information about newly characterized 16S or 23S rRNA mutations.

Recent develoments :
We plan to expand the database to include mutations in ribosomal proteins and ribosomal factors. The expanded database will be called The Ribosomal Mutation Database. Please send bibliographic citations for published work to be included in The Ribosomal Mutation Database to the curator by email at ktriman@fandm.edu.

Aknowledgement :
We are grateful to Janan Eppig, Carol Bult, and Debra Krupke from the Bioinformatics Group at the Jackson Laboratory for their expert advice on the use of appropriate database software. This work was supported by the National Science Foundation (MCB-9726951).

5S Ribosomal RNA Database

http://biobases.ibch.poznan.pl/5SData/

Description :
5S ribosomal RNA is an integral component of the large subunit of all cytoplasmic and most organellar ribosomes. Its small size and association with ribosomal as well as non-ribosomal proteins made it an ideal model RNA molecule for studies of RNA structure and RNA-protein interactions. 5S Ribosomal RNA Database provides information on nucleotide sequences of 5S rRNAs and their genes. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The databaes is available on line at http://biobases.ibch.poznan.pl/5SData/ .

European rRNA database

http://www.psb.ugent.be/rRNA/

Description :
All complete or nearly complete rRNA sequences

Greengenes

http://greengenes.lbl.gov/

Description :
An online full-length small-subunit (SSU) rRNA gene database called greengenes that keeps pace with public submissions of both archaeal and bacterial 16S rDNA sequences has been established. It addresses a number of limitations currently associated with SSU rRNA records in the public databases by providing automated chimera-screening, taxonomic placement of unclassified environmental sequences using multiple published taxonomies for each record, multiple standard alignments and uniform sequence-associated information curated from GenBank records. Manipulation of 72,918 rDNA records revealed putative chimeras in 5% (1,901 of 38,412) of environmental sequences and, surprisingly, 0.5% (201/36,643) of records derived from isolates. Greengenes also provides a suite of utensils for manipulation of sequences including an alignment tool and has been streamlined to interface with the widely used ARB program.

Recent develoments :
New tools are available for beta testing including advanced search and export features, graphical alignment viewer, sequencing read quality trimmer, sequence classifier, and a distance matrix generator. To improve the reliability of the inferred comprehensive 16S rDNA prokaryotic tree, RAxML-V has been implemented to determine the maximum likelihood of branch points. This should allow an attenuation of the disparate phylogenetic trees maintained by separate curators worldwide.

Aknowledgement :
Computational support is provided through the Virtual Institute for Microbial Stress and Survival (http://VIMSS.lbl.gov). This work was performed under the auspices of the US Department of Energy by the University of California, Lawrence Berkeley National Laboratory under Contract No. DE-AC03-76SF00098 and was funded in part by the Department of Homeland Security under grant number HSSCHQ04X00037 and in part by the Department of Energy Natural and Accelerated Bioremediation Program.

References :
1. DeSantis, T.Z., Dubosarskiy, I., Murray, S.R., and Andersen, G.L. (2003) Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. Bioinformatics 19(12), 1461-1468.

Ribosomal Database Project (RDP-II)

http://rdp.cme.msu.edu/

Description :
The Ribosomal Database Project - II (RDP-II)(1) provides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16,277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. Currently available on the RDP-II website as a beta release, 9.0 provides over 50,000 annotated (eu)bacterial sequences aligned with a secondary-structure based alignment algorithm (2). We feel these alignments are, for most purposes, of equal utility to hand-alignments, but without any unintended bias or other potential hand-alignment artifacts. At least monthly updates are scheduled for this new alignment, and similar alignments will be released for archaeal, eukaryotic, and mitochondrial small-subunit rRNA sequences. This new alignment can be displayed using either the taxonomy assigned by NCBI or in a schema closely matching the taxonomy proposed by Garrity et al. (3). Data subsets are available for sequences of length 1200 or greater and for sequences from type material. Annotation goals include up-to-date name, strain and culture deposit information, sequence length and quality information, references, and, in collaboration with Bergey's Trust (3), type status. In order to provide a phylogenetic context for the data, RDP-II makes available over 100 trees that span the phylogenetic breadth of life. Web based research tools are provided for comparing user submitted sequences to the RDP-II database (Sequence Match), aligning user sequences against the nearest RDP sequence (Sequence Aligner), examining probe and primer specificity (Probe Match), testing for chimeric sequences (Chimera Check), generating a distance matrix (Similarity Matrix), analyzing T-RFLP data (T-RFLP and TAP-TRFLP), a java-based phylogenetic tree browser (Sub Trees), a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). The latter tool has been enhanced to allow a choice of either the Phylip neighbor-joining (4) or Weighbor weighted neighbor-joining (5) programs for tree construction. In addition, the web-site includes an interactive tutorial to guide users through the basics of rRNA sequence analysis. This tutorial is suitable both for the researcher new to rRNA based phylogenetic analysis and as a teaching module for upper-level undergraduate and graduate classes. The RDP-II email address for questions or comments is rdpstaff@msu.edu

Recent develoments :
New to RDP-II this year are enhancements to allow tree-building using the Weighbor method, in addition to neighbor-joining, and a new (eu)bacterial alignment of over 50,000 rRNA sequences that is updated on a regular basis.The RDP (eu)bacterial alignment is updated monthly and now contains over 76,000 sequences.

Aknowledgement :
We thank several individuals for their past contributions: Robin Gutell (and his colleagues), Bonnie Maidak, Tim Lilburn, Niels Larson, Tom Macke, Michael J. McCaughey, Ross Overbeek, Sakti Pramanik, Scott Dawson, Mitch L. Sogin, Gary Olsen and Carl Woese. The US Department of Energy Office of Science and the State of Michigan currently support RDP-II.

References :
1. Maidak, B.L., Cole, J.R., Lilburn, T.G., Parker, C.T., Saxman, P.R., Farris, R.J., T.M., Garrity, G.M., Olsen, G.J., Schmidt, T.M. and Tiedje, J.M. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29,173-174.
2. Brown, M.P.S. (2000) Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammar. ISMB. 57-66.
3. Garrity, G.M., Winters, A., Kuo, A.W., and Searles, D.B. (2002) Taxonomic outline of the prokaryotes. Bergey's manual of systematic bacteriology, second edition. http://www.springer-ny.com/bergeysoutline
4. Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
5. Bruno, W.J., Socci, N.D., and Halpern, A.L. (2000) Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction. Mol. Biol. Evol. 17(1):189-197.

RISSC - Ribosomal Internal Spacer Sequence Collection

http://ulises.umh.es/RISSC

Description :
This is a database of ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics. It compiles more than 2500 entries of edited DNA sequence data from the 16S-23S ribosomal spacers present in most prokaryotes and organelles. Ribosomal spacers have proven to be extremely useful tools for typing and identifying closely related prokaryotes due to their high variability in size and/or sequence, much more so than the flanking 16S and 23S rRNA genes. These genes are commonly used to establish molecular relationships among microbes at a taxonomic level of species or higher (e.g genus, domain). However their internal transcribed spacers (ITS) are much more useful to discriminate at the species or even strain level. Currently, many published papers are showing the growing importance of these regions of the ribosomal operon in these types of studies. By creating RISSC, our intention is to provide the scientific community with a comprehensive set of ribosomal spacer sequences, fully edited and characterized with a key feature as is the presence/absence of tRNA genes within them, ready to be used and compared with their own ITS sequences. A second, much shorter, ribosomal spacer can be found between rRNA genes 23S and 5S, also of phylogenetic interest. We intend to incorporate them into the database in the near future.

The Small Subunit rRNA Modification Database

http://library.med.utah.edu/SSUmods/

Description :
Modified nucleosides in small subunit rRNA

probeBase

http://www.microbial-ecology.net/probebase/

Description :
probeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information. Rapid access to probe, microarray and reference data is achieved by powerful search tools and via different lists that are based on selected categories such as functional or taxonomic properties of the target organism(s), or the hybridization format (fluorescence in situ hybridization or microarray) in which the probes were applied. Additional information on probe coverage and specificity is available through direct submissions of probe sequences from probeBase to RDP-II and Greengenes, two major rRNA sequence databases. A freely-editable user comments field for each probe entry allows any user to add, modify, or remove information, or to report errors in real-time. probeBase entries increased from 700 to more than 1,200 during the past three years. Several options for submission of single probes or entire probe sets, even prior to publication of newly developed probes, should further contribute to keeping probeBase an up-to-date and useful resource.

Aknowledgement :
The authors are indebted to Safak Yilmaz and Daniel Noguera for calculation of the ΔG values. We greatly thank Todd DeSantis for his efforts to facilitate the access to Greengenes and acknowledge help of Christian Baranyi for statistical analysis and of Carmen Krammer, Manuela Hartmann, and Silvia Weber for database maintenance. We further thank Phil Hugenholtz for valuable comments and all users who contributed to probeBase by submitting probes.

References :
1. Loy, A., Maixner, F., Wagner, M., Horn, M. 2007. probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res., in press.
2. Loy, A., Horn, M., Wagner, M. 2003. probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res., 31, 514-516.

RRNDB

http://rrndb.cme.msu.edu/

Description :
The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database, hosted by the Center for Microbial Ecology at Michigan State University, which contains annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon on prokaryotic genomes, yet the rRNA genes can vary from 1 to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes on a genome is not readily accessible. In an attempt to understand the evolutionary and ecological implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed, and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using rRNA gene sequences.

PPNEMA - Plant-Parasitic Nematode rRNAs

http://bighost.area.ba.cnr.it/PPNEMA Plant-parasitic nematode rRNAs

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