Nucleic Acids Research Advance Access published online on November 11, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl837
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© 2006 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.
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fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan 2 Intec Web and Genome Informatics, 1-3-3 Shinsuna Koto-ku, Tokyo 136-0075, Japan 3 Information and Mathematical Science Laboratory, 1-5-21 Oh-tsuka, Bunkyo-ku, Tokyo 112-0012, Japan 4 Mitsubishi Research Institute, 2-3-6 O-temachi, Chiyoda-ku, Tokyo 100-8140, Japan 5 Department of Computational Biology, Graduate School of Frontier Sciences University of Tokyo, 5-1-5 Kashiwa-no-ha, Chiba 277-8583, Japan
*To whom correspondence should be addressed. Tel: +81 3 355 8059; Fax: +81 3 355 8081; Email: kin-taushin{at}aist.go.jp
Received August 15, 2006. Revised September 20, 2006. Accepted October 6, 2006.
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/
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