Bioinformatics tools for lncRNA research

Junichi Iwakiri; Michiaki Hamada; Kiyoshi Asai

doi:10.1016/j.bbagrm.2015.07.014

Bioinformatics tools for lncRNA research

Biochim Biophys Acta. 2016 Jan;1859(1):23-30. doi: 10.1016/j.bbagrm.2015.07.014. Epub 2015 Aug 10.

Authors

Junichi Iwakiri¹, Michiaki Hamada², Kiyoshi Asai³

Affiliations

¹ 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.
² 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.
³ 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.

PMID: 26271403
DOI: 10.1016/j.bbagrm.2015.07.014

Abstract

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.

Keywords: Conservation; Expression; Mapping; Secondary structure; lncRNA.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Computational Biology*
Databases, Genetic
Humans
Nucleic Acid Conformation*
RNA, Long Noncoding / chemistry
RNA, Long Noncoding / genetics*
Transcriptome

Substances

RNA, Long Noncoding