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Project name Functional RNA Project
Area Genome Informatics
Purpose

The objective of this project is to establish the leadership of Japan in this research field by developing methods to estimate functional RNAs using bioinformatics as well as supporting techniques and tools for analyzing functional RNAs and analyzing the functions of functional RNAs. Another purpose of the project is to contribute to the creation of new medical/diagnostic business fields through timely utilization of patents based on the results of the project. (cited from the "NEDO:Functional RNA Project" (http://www.nedo.go.jp/english/activities/portal/gaiyou/p06011/p06011.html))
Introduction

Through recent research activities, it has been found that there are many noncoding RNAs (ncRNA) that can undergo transcription although they do not code proteins, unlike conventional RNAs that code proteins, in the cells of higher organisms, including mammals. These noncoding RNAs play an important role as functional RNAs in the processes of development and differentiation of cells. Moreover, it is understood that these RNAs are deeply involved in the development of various diseases, including cancer and diabetes. The objective of this project is to establish the leadership of Japan in this research field by developing methods to estimate functional RNAs using bioinformatics as well as supporting techniques and tools for analyzing functional RNAs and analyzing the functions of functional RNAs. Another purpose of the project is to contribute to the creation of new medical/diagnostic business fields through timely utilization of patents based on the results of the project. (cited from the "NEDO:Functional RNA Project" (http://www.nedo.go.jp/english/activities/portal/gaiyou/p06011/p06011.html))
Keyword functional RNA | non-coding RNA | Bioinformatics | functional analysis | tool development
Started fiscal year 2005-2009
Project head Kimitsuna Watanabe
Institute of the head Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST)
Budget (million yen) 4000
Representative Institute of the commission Japan Biological Informatics Consortium (JBiC)
Companies Japan Biological Informatics Consortium (JBiC) | Kyowa Hakko | Mizuho Information & Research Institute, Inc. | INTEC Systems Institute, Inc. | DNA Chip Research Inc.
Published papers (PubMed IDs) 16908501 | 17459961 | 18056736 | 18948287
Patent (Japan, overseas) Under investigation
Archives
The progress report on "Functional RNA Project" 2006-2008. Japanese.

Product (Database, Tool)

CentroidAlifold

Summary CentroidAlifold provides Accurate (common) secondary structure prediction for aligned RNA sequences. You can download CentroidAlifold software , which was contained in CentroidFold package (cited from the original site).
Data type RNA secondary structure

CentroidAlign

Summary An accurate and fast aligner for multiple RNA sequences, based on maximizing the expected sum-of-pair score (SPS).　You can get the archive file for linux and windows (cited from the original site).
Data type RNA alignment

CentroidFold

Summary CentroidFold is a software to predict RNA second structure and common second structure. A benchmark test shows it performs better than Mfold and RNAfold.
Data type RNA

CentroidHomfold

Summary CentroidHomfold provides RNA Secondary Structure prediction using Homologous Sequences. You can download CentroidHomfold software, which was contained in CentroidFold, or use CentroidHomfold-LAST Web-Server (cited from the original site).
Data type secondary structure

MXSCARNA

Summary MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA.
Data type RNA (RNA sequence)

Murlet

Summary Murlet is a multiple alignment tool for RNA sequences using iterative alignment based on Sankoff's algorithm with sharply reduced computational time and memory. This was developed by Computational Biology Research Center (CBRC), AIST.
Data type RNA

PHMMTS

Summary PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure (cited from the original site).
Data type RNA

PSTAG

Summary PSTAG (Pair Stochastic Tree Adjoining Grammars) is for RNA sequences including pseudoknotted structures.The program based on PSTAGs is the first grammar-based and practically executable software for comparative analyses of RNA pseudoknot structures, and, further, non-coding RNAs (cited from the original site).
Data type RNA

RNAmine

Summary
Data type RNA

Rfold

Summary
Data type RNA

Stem Kernels

Summary Stem Kernels is a kernel function for structural RNAs to measure a kind of similarity between a pair of RNA sequences from the viewpoint of secondary structures (cited from the original site).
Data type RNA

The Functional RNA Sequence Database

Summary fRNAdb is a sequence database hosting a large collection of non-coding RNA sequence data from public non-coding databases. fRNAdb allows users to search the sequences through keywords associated with them. Various kinds of information are associated with a sequence. fRNAdb also provides sequence homology search using Blastn.
Data type RNA

UCSC GenomeBrowser for Functional RNA

Summary UCSC GenomeBrowser for Functional RNA is a UCSC Genome Browser mirror with large additional custom tracks specifically associated with non-coding elements. It also includes several functional enhancements such as a presentation of a common secondary structure prediction at any given genomic window <500 bp.
Data type Comparative genomics

miRRim

Summary miRRim is a method for detecting miRNA foldbacks based on hidden Markov model (HMM). In this method, the evolutionary and secondary structural features of a miRNA region is represented by a sequence of multidimensional vectors. HMMs that generate a sequence of continuous values are used to model the feature vector sequences.(cited from the original site)
Data type RNA 　(miRNA)

Relating project

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