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Abstract

MicroRNAs (miRNAs) are endogenous, small, noncoding RNAs of 18-25 nucleotides in length that negativelyregulate their complementary messenger-RNAs at the post transcriptional level. Presently there are three approachesfor miRNA identification. Two approaches i.e. bioinformatic and small RNA library construction and sequencingare examples of reverse genetics approach. In these two approaches researchers try to find miRNAs in the knowngenotypes (sequences). A third approach called the classical approach is example of forward genetics in whichresearchers determine the unknown genotype (miRNA sequence) of a known phenotype. The miRNAs have shownboth evolutionarily converged nature (conserved miRNAs) from species to species within the same kingdom andspecies specific expression (species specific miRNAs). Majority of the miRNA genes are observed as conservedmiRNAs as orthologs. This conserved nature of majority of miRNAs becomes an important logical tool forbioinformatics discovery of miRNAs in other species. Identification of miRNAs by using bioinformatic tools is nowa commonplace and of the most widely used methods and it has facilitated the prediction of new miRNAs in bothplant and animal systems. This is largely used due to its low cost and high efficiency. In 2001 the 1st release ofmiRBases (an online repository of miRNAs) contained only 218 miRNA entries and now its latest release 20(released in June 2013) contains 24521 entries. The bioinformatics hunting of miRNAs has also a reasonablecontribution in identification of new miRNAs. Around 25% of entries in miRBase (across all species) are predictedcomputationally. Likewise in Plant MicroRNA Database (PMRD) within the total 8433 miRNAs, 1297 of them areexperimentally demonstrated and 7136 of them are from computational predictions . This review is aimed atdescribing the bioinformatic resources used in miRNA identification. Furthermore, the limitations of these resourcesare also described.
Keywords: Bioinformatics, Comparative genomics, MicroRNA
http://dx.doi.org/10.19045/bspab.2014.32004