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The Small Subunit rRNA Modification Database
James A McCloskey1, Jef Rozenski
1Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
Nucleic Acids Research
|December 21, 2004
Summary
The Small Subunit rRNA Modification Database catalogs modified nucleosides and their locations in ribosomal RNA across bacteria, archaea, and eukarya. This resource aids researchers studying RNA modifications and phylogenetic relationships.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genomics
Background:
- Ribosomal RNA (rRNA) undergoes extensive post-transcriptional modifications crucial for its structure and function.
- Understanding these modifications is vital for deciphering gene expression and cellular processes across diverse life forms.
Purpose of the Study:
- To create a centralized, accessible database of small subunit (SSU) rRNA modifications.
- To compile and present data on modified nucleosides and their sequence sites from various organisms.
Main Methods:
- Data compilation from published rRNA sequences and oligonucleotide catalogs.
- Database curation and assembly of sequence maps using contemporary gene data.
- Organization of data by source organism and modification identity.
Main Results:
- A comprehensive listing of post-transcriptionally modified nucleosides in SSU rRNAs from bacteria, archaea, and eukarya.
- 32 annotated rRNA sequence alignments detailing modification sites and identities.
- Flexible data presentation including full sequence maps and tabular formats.
Conclusions:
- The Small Subunit rRNA Modification Database serves as a valuable resource for researchers in molecular biology and bioinformatics.
- Facilitates comparative analysis of RNA modifications and phylogenetic studies.
- Provides a foundation for further investigation into the functional roles of rRNA modifications.