pssRNAMiner

PssRNAMiner is a software tool developed to detect both the clusters of phased small RNAs and the potential phase-initiator in plants. The software tool is designed to identify the miRNA --> ta-siRNA --> target gene cascade pathway that regulates gene expression at the posttranscriptional level.

This cascade pathway is composed of short RNAs, including approximately 21-nt microRNA (miRNA) and 21-nt trans-acting siRNA (ta-siRNA), that require 21-nt intervals (i.e., phasing) and miRNA (phase-initiator) cleavage sites on its TAS transcript to biogenesis ta-siRNA clusters. The pssRNAMiner web server maps input small RNAs against user-specified transcript/genomic sequences and identify phased small RNA clusters by evaluating P-values of the hypergeometric distribution.

The PssRNAMiner software tool aligns input phase-initiators with transcripts of TAS candidates using the Smith-Waterman algorithm to identify potential cleavage sites on TAS candidates. Potential cleavage sites on TAS candidates are further identified from complementary regions by weighting the alignment expectation and its distance to detected phased small RNA clusters.