pssRNAMiner

pssRNAMiner identifies trans-acting small interfering RNA (ta-siRNA) clusters and their potential phase initiators in plant transcript-genomic sequences to characterize miRNA → ta-siRNA → target gene posttranscriptional regulatory cascades.

Key Features:

• Identification of Phased Small RNA Clusters: Maps user-provided small RNA datasets against specified transcript-genomic libraries and detects phased small RNA clusters using P-values from the hypergeometric distribution.
• Detection of Potential Phase-Initiators: Aligns input phase-initiator sequences to TAS transcripts using the Smith-Waterman algorithm and identifies potential cleavage sites by analyzing complementary regions, alignment expectations, and proximity to phased small RNA clusters.

Scientific Applications:

• Posttranscriptional Gene Regulation in Plants: Enables identification of ta-siRNA clusters and phase initiators to study miRNA-mediated posttranscriptional regulation.
• Regulatory Cascade Elucidation and Functional Genomics: Supports characterization of the miRNA → ta-siRNA → target gene cascade for applications in plant genetics, molecular biology, and biotechnology.

Methodology:

Mapping of input small RNAs to user-specified transcript-genomic sequences; phasing analysis with hypergeometric-distribution P-values to identify phased clusters; Smith-Waterman alignment of phase-initiators to TAS transcripts; identification of potential cleavage sites by analysis of complementary regions and proximity to phased small RNA clusters.