Bioinformatics tools for lncRNA research.
Current experimental methods to identify the functions of a large number of the candidates of long non-coding RNAs (lncRNAs) are limited in their throughput. Therefore, it is essential to know which tools are effective for understanding lncRNAs so that reasonable speed and accuracy can be achieved. In this paper, we review the currently available bioinformatics tools and databases that are useful for finding non-coding RNAs and analyzing their structures, conservation, interactions, co-expressions and localization. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan; Computational Biology Research Consortium (CBRC), in National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan.
Junichi
J
Iwakiri
Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55 N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan; Computational Biology Research Consortium (CBRC), in National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan.
Michiaki
M
Hamada
Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan; Computational Biology Research Consortium (CBRC), in National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan. Electronic address: asai@k.u-tokyo.ac.jp.
Kiyoshi
K
Asai
D019295:Computational Biology; D030541:Databases, Genetic; D006801:Humans; D009690:Nucleic Acid Conformation; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics*; D059467:Transcriptome
D062085:RNA, Long Noncoding
Conservation; Expression; Mapping; Secondary structure; lncRNA