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Updated: Jun 28, 2026
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
Toutai Mituyama1, Kouichirou Yamada, Emi Hattori
1National Institute of Advanced Industrial Science and Technology, Computational Biology Research Center, Tokyo 135-0064, Japan. mituyama-toutai@aist.go.jp
Nucleic Acids Research
|October 25, 2008
Summary
We created the Functional RNA Database (fRNAdb) to help annotate RNA transcripts and discover new non-coding RNAs. This enhanced resource offers improved sequence data and advanced visualization tools for researchers.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Non-coding RNAs (ncRNAs) play crucial roles in gene regulation.
- Accurate annotation and discovery of ncRNAs are essential for understanding cellular functions.
- Existing databases often lack comprehensive data or user-friendly interfaces for ncRNA research.
Purpose of the Study:
- To develop an integrated database resource for the annotation of RNA transcripts.
- To facilitate the discovery of novel non-coding RNAs.
- To provide enhanced tools for ncRNA data visualization and analysis.
Main Methods:
- Developed a rewritten version of the Functional RNA Database (fRNAdb) as a sequence database.
- Created a mirror of the UCSC Genome Browser with custom tracks for functional RNA data.
- Integrated secondary structure prediction capabilities for genomic windows up to 500 bp.
- Implemented user authentication and support for user-specific tracks.
Main Results:
- The new fRNAdb hosts a significantly larger collection of known, predicted, and novel ncRNA sequences.
- The enhanced Genome Browser offers more tracks and richer features, including secondary structure visualization.
- The combined database provides a more powerful and user-friendly platform for ncRNA research.
Conclusions:
- The Functional RNA Database offers a valuable, integrated resource for ncRNA annotation and discovery.
- The enhanced visualization and data accessibility will accelerate research in ncRNA function and regulation.
- The database is publicly available at http://www.ncrna.org/.
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