Chapter 5 - Methods for Identifying Small RNA Genes

摘要: Abstract As ubiquitous regulators of gene expression, small RNAs have been found in almost all eukaryotic organisms. Identification RNA genes remains an important but difficult task. In this review, we summarize strategies for finding using computational approaches, with emphasis on microRNAs (miRNAs). Methods preprocessing different types sequence data, which are necessary to increase the reliability and efficiency, introduced. Homology searches conserved miRNAs de novo prediction novel described detail. Because high false-positive rates these experimental validation predicted is necessary. Northern blots quantitative real-time PCR (qPCR) analyses good choices validating expression vitro a scale, whereas reporter assays suitable vivo studies. its higher sensitivity, microarray analysis efficient examining levels at large scale. Algorithms predicting miRNA targets also summarized. such as assays, knockdown, ablation biogenesis proteins, microarrays developed validate target sites either one-by-one or high-throughput level. Furthermore, present brief introduction methods identifying Piwi-interacting by experiments prediction. The advantages disadvantages techniques discussed.