Fruitfly

One critical step in RNA interference (RNAi) experiments is to design small interfering RNAs (siRNAs) that can greatly reduce the expression of the target transcripts, but not of other unintended targets. Although various statistical and computational approaches have been attempted, this remains a challenge facing RNAi researchers. Here, we present a new experimentally validated method for siRNA design.

Small RNA RNA-seq for microRNAs (miRNAs) is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries.

MicroRNAs (miRNAs) are small non-coding single-stranded RNAs (20-23 nts) that are known to act as post-transcriptional and translational regulators of gene expression. Although, they were initially overlooked, their role in many important biological processes, such as development, cell differentiation, and cancer has been established in recent times. In spite of their biological significance, the identification of miRNA genes in newly sequenced organisms is still based, to a large degree, on extensive use of evolutionary conservation, which is not always available.

miRNAs are small non coding RNA structures which play important roles in biological processes. Finding miRNA precursors in genomes is therefore an important task, where computational methods are required. The goal of these methods is to select potential pre-miRNAs which could be validated by experimental methods. With the new generation of sequencing techniques, it is important to have fast algorithms that are able to treat whole genomes in acceptable times.