The rrnDB is a curated database that catalogs the numbers of genes that encode for 16S and 23S ribosomal RNAs in Bacteria and Archaea.
http://rrndb.umms.med.umich.edu/
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rrnDB - the Ribosomal RNA Operon Copy Number Database - Homepage | rrndb.umms.med.umich.edu Reviews
https://rrndb.umms.med.umich.edu
The rrnDB is a curated database that catalogs the numbers of genes that encode for 16S and 23S ribosomal RNAs in Bacteria and Archaea.
rrndb.umms.med.umich.edu
About rrnDB
https://rrndb.umms.med.umich.edu/about
The Ribosomal RNA Database. Curated by the Schmidt Laboratory. The ribosomal RNA operon copy number database is a publicly available, curated resource for ribosomal operon ( rrn. Copy number information for Bacteria and Archaea. Previous releases of rrn. DB are described in the following publications:. Stoddard S.F, Smith B.J., Hein R., Roller B.R.K. and Schmidt T.M. (2015) rrn. 2014; doi: 10.1093/nar/gku1201. [ PMID:25414355. Lee,ZM., Bussema,C. 3rd and Schmidt,T.M. (2009) rrn. Hashimoto, J.G., ...Klapp...
About Versions
https://rrndb.umms.med.umich.edu/about_versions
The Ribosomal RNA Database. Curated by the Schmidt Laboratory. DB Version Number System:. The leftmost number represents a major internal change by rrn. The date and version of each of the major data sources that are used to build rrn. DB are shown for each rrn. DB version. Data source versions do not always change in concert with increments in the rrn. DB version. For example the rrn. Data source release dates. RDP Classifier training set. Jan 19, 2017. Jan 19, 2017. RDP Classifier 2.12. Oct 17, 2016.
Download
https://rrndb.umms.med.umich.edu/static/download
The Ribosomal RNA Database. Curated by the Schmidt Laboratory. DB's current and previous data sets are made available here for download as individual files in tab-delimited format. For information about current and previous versions of rrn. DB see the About rrn. RrnDB-5.1 pantaxa stats RDP.tsv.zip. Pan-taxa statistics for RDP taxonomy. RrnDB-5.1 pantaxa stats NCBI.tsv.zip. Pan-taxa statistics for NCBI taxonomy. RrnDB-5.1.tsv.zip. RrnDB-5.0 pantaxa stats RDP.tsv.zip. Pan-taxa statistics for RDP taxonomy.
rrnRB Estimate
https://rrndb.umms.med.umich.edu/estimate
The Ribosomal RNA Database. Curated by the Schmidt Laboratory. Estimate is an on-line interface to the RDP Classifier tool, including adjustment of relative abundance of taxons based on 16S gene copy number data from rrn. Estimate produces three output files; one for the sequence classifications and two. Files containing the unadjusted and copy-number-adjusted relative abundance of taxons. The filename of the adjusted copy number data will be prefixed. With one derived from the most recent downloadable.
rrnDB Manual
https://rrndb.umms.med.umich.edu/help
The Ribosomal RNA Database. Curated by the Schmidt Laboratory. How to use rrn. Look up a specific taxon. Search by 16S copy number. Keyword search of record annotations. Uploading a FASTA file and running RDP Classifier. Searching the database [ contents. There are several different ways in which the database can be searched. All these ways are accessible on the main search page reachable via the. Link on the navigation menu. If you are interested in information about a specific taxon:. Search field, the...
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Related Sites
http://rdp.cme.msu.edu/misc/related.jsp
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. 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. The Integrate...
Classifier
http://rdp.cme.msu.edu/classifier/classifier.jsp
NEW procedural tutorials for CLASSIFIER. Classifier now provides gene copy number adjustment. For 16S gene sequences. The 16S gene copy number data is provided by rrnDB. For detailed analysis. The Warcup V2 release notes. Is released in June 2016. How to cite Classifier? The RDP Classifier publication has been selected by Essential Science Indicators as the most-cited paper in a highlighted research area of microbiology. It's featured in December 2011 Science Watch. Please enter your sequences:. MSU is a...
Links | probeBase 2016
http://probebase.csb.univie.ac.at/node/3
Ribosomal RNA-related web resources. A software environment for sequence data. 16S rRNA database and online analysis tools; ARB compatible. The Ribosomal Database Project II (RDP). 16S rRNA database and online analysis tools. 16S rRNA database and ARB compatible online-workbench. A resource for evaluating probe and primer specificity. A web tool for the computational evaluation of RNA-targeted FISH probes and primers. The All-Species Living Tree' Project. RRNA Operon Number Database. The RNA World Website.
Related Sites
http://nightingale.cme.msu.edu/misc/related.jsp
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. 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. The Integrate...
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rrnDB - the Ribosomal RNA Operon Copy Number Database - Homepage
The Ribosomal RNA Database. Curated by the Schmidt Laboratory. Version 4.3.3. November 06, 2014. A searchable database documenting variation in ribosomal RNA operons ( rrn. In Bacteria and Archaea. Find information such as the 16S gene copy number of an organism by looking up its name under the NCBI or RDP taxonomy or by full-text search of rrn. Please cite the use of rrn. DB in the following way:. Roller B.R.K. And Schmidt T.M. Doi: 10.1093/nar/gku1201 [ PMID:25414355. And full text [ HTML.
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