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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
Published on: December 2, 2009
rrndb: the Ribosomal RNA Operon Copy Number Database
J A Klappenbach1, P R Saxman, J R Cole
1Department of Microbiology and Molecular Genetics and Center for Microbial Ecology, Michigan State University, 203 Giltner Hall, East Lansing, MI 48824-1101, USA.
Nucleic Acids Research
|January 11, 2000
Summary
The Ribosomal RNA Operon Copy Number Database (rrndb) provides accessible data on prokaryotic rRNA gene copy numbers. This resource aids researchers studying microbial evolution and ecology using 16S rRNA gene sequences.
Area of Science:
- Microbiology
- Bioinformatics
- Evolutionary Biology
Background:
- Prokaryotic genomes typically have low gene redundancy, but rRNA genes can range from one to 15 copies.
- 16S rRNA gene sequences are widely used for prokaryotic identification, yet comprehensive data on rRNA gene copy number and sequence is not readily available.
- Understanding rRNA operon redundancy is crucial for evolutionary studies.
Purpose of the Study:
- To create a centralized, accessible database of rRNA operon copy numbers in prokaryotes.
- To facilitate research into the evolutionary implications of rRNA gene redundancy.
- To provide a valuable resource for microbial ecology and evolution researchers.
Main Methods:
- Compilation of annotated information on rRNA operon copy number from diverse prokaryotic microorganisms.
- Phylogenetic arrangement of data within the database.
- Linking entries to external resources like GenBank, PubMed, and culture collections.
Main Results:
- Development of the Ribosomal RNA Operon Copy Number Database (rrndb).
- The database contains phylogenetically organized information on rRNA gene copy number for a wide range of prokaryotes.
- Each entry provides direct links to external, relevant biological databases and resources.
Conclusions:
- The rrndb serves as a valuable, accessible resource for researchers in microbial ecology and evolution.
- The database aids in understanding the evolutionary significance of rRNA operon copy number variation in prokaryotes.
- Facilitates comparative genomics and phylogenetic analyses utilizing rRNA gene information.
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