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Bioinformatics Databases and Tools on Dietary MicroRNA

  • Juan CuiEmail author
Reference work entry

Abstract

Empowered by the emerging genomics technology, there has been an increasingly large accumulation of noncoding RNA information, particularly on microRNAs in animals and plants. Research interest in microRNAs originating from food mostly focused on their bioavailability and cross-species transportation and regulation has recently grown due to the potential implication of regulatory role and cofounding impact in human health. This chapter reviews publicly available repositories and bioinformatics tools developed for dietary microRNA research, including the first dietary microRNA database (DMD) that archives microRNA sequence and annotation in various dietary sources, a new small RNA sequencing analytical pipeline focusing on the detection of both endogenous and exogenous microRNAs, and other general computational resources and tools for microRNA target prediction and functional analysis.

Keywords

Dietary microRNA Exogenous microRNA Bioinformatics microRNA target prediction Small RNA sequencing Dietary microRNA database (DMD) microRNA function microRNA transportation Exosome Gene regulation network Sequence motif 

List of Abbreviations

DMD

Dietary microRNA database

miRs, miRNAs

microRNAs

pre-miRNA

Precursor microRNA

NGS

Next-generation sequencing

KEGG

Kyoto Encyclopedia of Genes and Genomes

PPI

Protein-protein interaction

RPKM

Reads Per Kilobase of transcript per Million mapped reads

MFE

Minimum free energy

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Computer Science and EngineeringUniversity of Nebraska-LincolnLincolnUSA

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