Kin Taishin, Yamada Kouichirou, Terai Goro, Okida Hiroaki, Yoshinari Yasuhiko, Ono Yukiteru, Kojima Aya, Kimura Yuki, Komori Takashi, Asai Kiyoshi
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan.
Nucleic Acids Res. 2007 Jan;35(Database issue):D145-8. doi: 10.1093/nar/gkl837. Epub 2006 Nov 11.
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/
存在大量不编码特定蛋白质且功能未明确的转录本。其中一些转录本可能具有新功能，而其他的可能是垃圾转录本。不幸的是，对这类转录本进行实验验证以寻找功能性非编码RNA候选物的成本非常高。因此，我们的主要兴趣是从一组未表征的转录本中通过计算挖掘候选功能性转录本。我们引入了fRNAdb：一种新颖的数据库服务，它存储了大量非编码转录本，包括来自H-inv数据库、NONCODE和RNAdb的注释/未注释序列。已对所包含的序列进行了一系列计算分析。这些分析包括RNA二级结构基序发现、EST支持评估、顺式调控元件搜索、蛋白质同源性搜索等。fRNAdb提供了一个高效的界面，帮助用户根据自己的标准筛选出特定的转录本，以挑选出功能性RNA候选物。可通过http://www.ncrna.org/访问fRNAdb
