miR-Explore: Predicting MicroRNA Precursors by Class Grouping and Secondary Structure Positional Alignment

Abstract

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expressions by targeting the mRNAs especially in the 3'UTR regions. The identification of miRNAs has been done by biological experiment and computational prediction. The computational prediction approach has been done using two major methods: comparative and noncomparative. The comparative method is dependent on the conservation of the miRNA sequences and secondary structure. The noncomparative method, on the other hand, does not rely on conservation. We hypothesized that each miRNA class has its own unique set of features; therefore, grouping miRNA by classes before using them as training data will improve sensitivity and specificity. The average sensitivity was 88.62% for miR-Explore, which relies on within miRNA class alignment, and 70.82% for miR-abela, which relies on global alignment. Compared with global alignment, grouping miRNA by classes yields a better sensitivity with very high specificity for pre-miRNA prediction even when a simple positional based secondary and primary structure alignment are used.

Keywords: chicken; miR-explore; miRNA; miRNA class alignment.

Figure 1

An example of alignment output from MARNA where ‘(’ and ‘)’ indicates the stem in the secondary structure, ‘.’ is a mismatch and ‘—’ is a gap.