The portal site for the Funtional RNA Project

This site hosts databases and bioinformatics tools developed by the bioinformatics group of the Functional RNA Project which is funded by New Energy and Industrial Technology Development Organization since 2005.

Databases

Ver. 3.0

The Functional RNA Database (fRNAdb) is a database for comprehensive non-coding RNA sequences including known non-coding RNAs, which are gathered from other sequence databases and original non-coding RNA sequences reported by the research groups joined for the Functional RNA Project.

Ver. 3.0

UCSC Genome Browser mirror with large inclusion of functional RNA related custom tracks and several enhancements for RNA secondary structure support.

Project Specific Custom Tracks

Table of custom tracks added by the functional RNA project.

The Contents of Genome presents major components of a genome at a glance. The major components are repeat elements, intergenic regions, and coding genes. Base size of each component is shown in a pie chart and a table. Each component is devided into subclasses and families, and further details of the components are presented. Enjoy!

RNA Bibliography

hosts a collection of journal articles related to RNAs.

Bioinformatics tools

software.ncrna.org

Our bioinformatics tools for RNA sequence analysis with web servers and source codes.

CentroidFold

CentroidFold predicts an RNA secondary structure from an RNA sequence. FASTA and one-sequence-in-a-line format are accepted for predicting a secondary structure per sequence. It also predicts a consensus secondary structure when a multiple alignment (CLUSTALW format) is given.

Idiographica

Idiographica is a web server for you to create your own idiograms on-demand.

Knowledgebase

Bioinformatics Tools

A classified list of Bioinformatics tools for RNA analysis.

Known ncRNAs

A comprehensive list of GenomeBrowser views for known ncRNAs in human genome.

Paper Review

Bioinformatics group of the Functional RNA Project have meeting on every Friday for reviewing journal papers related to RNA, Bioinformatics, machine learning and so on. Here we let some our handouts (usually written in Japanese) open for access.