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MetaMirClust: Discovery and Exploration of Evolutionarily Conserved miRNA Clusters

  • Wen-Ching ChanEmail author
  • Wen-chang Lin
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1375)

Abstract

Recent emerging studies suggest that a substantial fraction of microRNA (miRNA) genes is likely to form clusters in terms of evolutionary conservation and biological implications, posing a significant challenge for the research community and shifting the bottleneck of scientific discovery from miRNA singletons to miRNA clusters. In addition, the advance in molecular sequencing technique such as next-generation sequencing (NGS) has facilitated researchers to comprehensively characterize miRNAs with low abundance on genome-wide scale in multiple species. Taken together, a large scale, cross-species survey of grouped miRNAs based on genomic location would be valuable for investigating their biological functions and regulations in an evolutionary perspective. In the present chapter, we describe the application of effective and efficient bioinformatics tools on the identification of clustered miRNAs and illustrate how to use the recently developed Web-based database, MetaMirClust (http://fgfr.ibms.sinic.aedu.tw/MetaMirClust) to discover evolutionarily conserved pattern of miRNA clusters across metazoans.

Keywords:

MetaMirClust microRNA cluster Data mining Synteny 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Kaohsiung Chang Gung Memorial HospitalKaohsiungRepublic of China
  2. 2.Institute of Biomedical Sciences, Academia SinicaTaipeiRepublic of China
  3. 3.Institute of Plant and Microbial Biology, Academia SinicaTaipeiRepublic of China

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