RIblast

an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach

Tsukasa Fukunaga, Michiaki Hamada

    Research output: Contribution to journalArticle

    16 Citations (Scopus)

    Abstract

    Motivation: LncRNAs play important roles in various biological processes. Although more than 58 000 human lncRNA genes have been discovered, most known lncRNAs are still poorly characterized. One approach to understanding the functions of lncRNAs is the detection of the interacting RNA target of each lncRNA. Because experimental detections of comprehensive lncRNA-RNA interactions are difficult, computational prediction of lncRNA-RNA interactions is an indispensable technique. However, the high computational costs of existing RNA-RNA interaction prediction tools prevent their application to large-scale lncRNA datasets.

    Results: Here, we present 'RIblast', an ultrafast RNA-RNA interaction prediction method based on the seed-and-extension approach. RIblast discovers seed regions using suffix arrays and subsequently extends seed regions based on an RNA secondary structure energy model. Computational experiments indicate that RIblast achieves a level of prediction accuracy similar to those of existing programs, but at speeds over 64 times faster than existing programs.

    Availability and implementation: The source code of RIblast is freely available at https://github.com/fukunagatsu/RIblast .

    Contact: t.fukunaga@kurenai.waseda.jp or mhamada@waseda.jp.

    Supplementary information: Supplementary data are available at Bioinformatics online.

    Original languageEnglish
    Pages (from-to)2666-2674
    Number of pages9
    JournalBioinformatics (Oxford, England)
    Volume33
    Issue number17
    DOIs
    Publication statusPublished - 2017 Sep 1

    Fingerprint

    Long Noncoding RNA
    RNA
    Seed
    Seeds
    Prediction
    Interaction
    Suffix Array
    RNA Secondary Structure
    Energy Model
    Computational Experiments
    Computational Cost
    Bioinformatics
    Availability
    Contact
    Gene
    Biological Phenomena
    Target
    Computational Biology
    Genes
    Costs and Cost Analysis

    ASJC Scopus subject areas

    • Statistics and Probability
    • Biochemistry
    • Molecular Biology
    • Computer Science Applications
    • Computational Theory and Mathematics
    • Computational Mathematics

    Cite this

    RIblast : an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach. / Fukunaga, Tsukasa; Hamada, Michiaki.

    In: Bioinformatics (Oxford, England), Vol. 33, No. 17, 01.09.2017, p. 2666-2674.

    Research output: Contribution to journalArticle

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