fRNAdb


18948287	The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. [PMID: 18948287] Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K. Abstract 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 < or =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/. Nucleic Acids Res. 2009:37(Database issue) \| 89 Citations (from Europe PMC, 2025-03-22)
17099231	fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. [PMID: 17099231] Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K. Abstract There are abundance of transcripts that code for no particular protein and that remain functionally uncharacterized. Some of these transcripts may have novel functions while others might be junk transcripts. Unfortunately, the experimental validation of such transcripts to find functional non-coding RNA candidates is very costly. Therefore, our primary interest is to computationally mine candidate functional transcripts from a pool of uncharacterized transcripts. We introduce fRNAdb: a novel database service that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences from the H-inv database, NONCODE and RNAdb. A set of computational analyses have been performed on the included sequences. These analyses include RNA secondary structure motif discovery, EST support evaluation, cis-regulatory element search, protein homology search, etc. fRNAdb provides an efficient interface to help users filter out particular transcripts under their own criteria to sort out functional RNA candidates. fRNAdb is available at http://www.ncrna.org/ Nucleic Acids Res. 2007:35(Database issue) \| 98 Citations (from Europe PMC, 2025-03-22)

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. [PMID: 18948287]

Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K.

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 < or =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/.

Nucleic Acids Res. 2009:37(Database issue) | 89 Citations (from Europe PMC, 2025-03-22)

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. [PMID: 17099231]

Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K.

Abstract

There are abundance of transcripts that code for no particular protein and that remain functionally uncharacterized. Some of these transcripts may have novel functions while others might be junk transcripts. Unfortunately, the experimental validation of such transcripts to find functional non-coding RNA candidates is very costly. Therefore, our primary interest is to computationally mine candidate functional transcripts from a pool of uncharacterized transcripts. We introduce fRNAdb: a novel database service that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences from the H-inv database, NONCODE and RNAdb. A set of computational analyses have been performed on the included sequences. These analyses include RNA secondary structure motif discovery, EST support evaluation, cis-regulatory element search, protein homology search, etc. fRNAdb provides an efficient interface to help users filter out particular transcripts under their own criteria to sort out functional RNA candidates. fRNAdb is available at http://www.ncrna.org/

Nucleic Acids Res. 2007:35(Database issue) | 98 Citations (from Europe PMC, 2025-03-22)

URL:	http://www.ncrna.org/
Full name:	Functional RNA Database
Description:	The Functional RNA Database is a database to support mining and annotation of functional RNAs.
Year founded:	2007
Last update:
Version:	v3.0
Accessibility:	Unaccessible
Country/Region:	Japan

Data type:	RNA
Data object:	NA
Database category:	Gene genome and annotation
Major species:	NA
Keywords:	functional RNAs

University/Institution:	National Institute of Advanced Industrial Science and Technology
Address:	National Institute of Advanced Industrial Science and Technology (AIST), Computational Biology Research Center (CBRC), Tokyo 135-0064, Japan
City:	Tokyo
Province/State:
Country/Region:	Japan
Contact name (PI/Team):	Toutai Mituyama
Contact email (PI/Helpdesk):	mituyama-toutai@aist.go.jp

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Database Commons a catalog of worldwide biological databases