Nucleic Acids Research Advance Access originally published online on October 23, 2008
Nucleic Acids Research 2009 37(Database issue):D89-D92; doi:10.1093/nar/gkn805
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Nucleic Acids Research, 2009, Vol. 37, Database issue D89-D92
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
1National Institute of Advanced Industrial Science and Technology (AIST), Computational Biology Research Center (CBRC), Tokyo 135-0064, 2Information and Mathematical Science Laboratory, Inc., Department of Life Sciences, Tokyo 112-0012, 3INTEC Systems Institute, Inc., Biobusiness Division, Tokyo 136-0075 and 4Graduate School of Frontier Sciences, Department of Computational Biology, University of Tokyo, Chiba 277-8583, Japan
*To whom correspondence should be addressed. Tel: +81 3 3599 8059; Fax: +81 3 3599 8081; Email: mituyama-toutai{at}aist.go.jp
Received September 13, 2008. Revised October 9, 2008. Accepted October 10, 2008.
We developed a pair of databases that support two important tasks: annotation of anonymous RNA transcripts and discovery of novel non-coding RNAs. The database combo is called the Functional RNA Database and consists of two databases: a rewrite of the original version of the Functional RNA Database (fRNAdb) and the latest version of the UCSC GenomeBrowser for Functional RNA. The former is a sequence database equipped with a powerful search function and hosts a large collection of known/predicted non-coding RNA sequences acquired from existing databases as well as novel/predicted sequences reported by researchers of the Functional RNA Project. The latter 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. Our GenomeBrowser supports user authentication and user-specific tracks. The current version of the fRNAdb is a complete rewrite of the former version, hosting a larger number of sequences and with a much friendlier interface. The current version of UCSC GenomeBrowser for Functional RNA features a larger number of tracks and richer features than the former version. The databases are available at http://www.ncrna.org/.
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