The Zhao Bioinformatics Laboratory
pssRNAMiner: A Plant Short Small RNA Regulatory Cascade Analysis Server  
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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.

The pssRNAMiner web server is freely available at

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Citation(s): Xinbin Dai and Patrick Xuechun Zhao. pssRNAMiner: A plant short small RNA regulatory cascade analysis server. Nucleic Acids Research 2008 Jul 1;36(Web Server issue):W114-8. Full Text


  © 2008 by The Samuel Roberts Noble Foundation, Inc.