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Nucleic Acids Research Advance Access originally published online on May 12, 2008
Nucleic Acids Research 2008 36(Web Server issue):W114-W118; doi:10.1093/nar/gkn297
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W114-W118
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

pssRNAMiner: a plant short small RNA regulatory cascade analysis server

Xinbin Dai and Patrick Xuechun Zhao*

Plant Biology Division, The Samuel Robert Noble Foundation, Ardmore OK 73401, USA

*To whom correspondence should be addressed. Tel: +1 580 224 6725; Fax: +1 580 224 6692; Email: pzhao{at}noble.org

Received February 2, 2008. Revised April 16, 2008. Accepted April 29, 2008.

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 posttranscriptional 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 http://bioinfo3.noble.org/pssRNAMiner/.


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