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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" 2006-2009. Japanese.

Product (Database, Tool)

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

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

RNAmine

Summary
Data type RNA

Rfold

Summary
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

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