A Review of Computational Tools in microRNA Discovery

Since microRNAs (miRNAs) were discovered, their impact on regulating various biological activities has been a surprising and exciting field. Knowing the entire repertoire of these small molecules is the first step to gain a better understanding of their function. High throughput discovery tools such as RNA-Seq significantly increased the number of known miRNAs in different organisms in recent years. However, the process of being able to accurately identify miRNAs is still a complex and difficult task, requiring the integration of experimental approaches with computational methods. A number of prediction algorithms based on characteristics of miRNA molecules have been developed to identify new miRNA species. Different approaches have certain strengths and weaknesses and in this review, the authors aim to summarize several commonly used tools in metazoan miRNA discovery.

Selected computational tools for miRNA prediction and their main characteristics.

Tool Website Year
miRscan genes.mit.edu/mirscan 2003
miRSeeker 2003
miRAlign bioinfo.au.tsinghua.edu.cn/miralign 2005
Phylogenetic shadowing 2005
ProMiR bi.snu.ac.kr/ProMiR 2005
Triplet-SVM bioinfo.au.tsinghua.edu.cn/software/mirnasvm 2005
miR-abela www.mirz.unibas.ch/cgi/pred_miRNA_genes.cgi 2005
RNAmicro www.bioinf.uni-leipzig.de/~jana/index.php/jana-hertel-software/65-jana-hertel-rnamicro 2006
miRFinder www.bioinformatics.org/mirfinder 2007
miPred www.bioinf.seu.edu.cn/miRNA 2007
MiRRim www.ncrna.org/software/miRRim 2007
miRDeep www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep 2008
miRanalyzer web.bioinformatics.cicbiogune.es/microRNA/miRanalyser.php 2009
SSCprofiler mirna.imbb.forth.gr/SSCprofiler.html 2009
HHMMiR http://www.benoslab.pitt.edu/kadriAPBC2009.html 2009
  • Gomes CP, Cho JH, Hood L, Franco OL, Pereira RW, Wang K. (2013) A Review of Computational Tools in microRNA Discovery. Front Genet 4, 81. [article]