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pssRNAMiner: A plant short small RNA regulatory cascade analysis server

In plants, short RNAs including ~21-nt microRNA (miRNA) and 21-nt trans-acting siRNA (ta-siRNA) compose a "miRNA -> ta-siRNA -> target gene" cascade pathway that regulates gene expression at the post-transcriptional level. In this cascade, biogenesis of ta-siRNA clusters requires 21-nt intervals (i.e. phasing) and miRNA (phase-initiator) cleavage sites on its TAS transcript. Here we report a novel web server, pssRNAMiner, which is developed to identify both the clusters of phased small RNAs as well as the potential phase-initiator.

  • To detect phased small RNA clusters, the pssRNAMiner maps input small RNAs against user-specified transcript/genomic sequences, and then identifies phased small RNA clusters by evaluating P values of hypergeometric distribution.
  • To identify potential phase-initiators, pssRNAMiner aligns input phase-initiators with transcripts of TAS candidates using the Smith-Waterman algorithm. 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.

» Visit pssRNAMiner


Copyright © 2007 by The Samuel Roberts Noble Foundation, Inc.