pssRNAMiner -- a plant short small RNA regulatory cascade analysis server
What you can do:
Identify both the clusters of phased small RNAs as well as the potential phase-initiator.
Highlights:
- In plants, short RNAs including approximately 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.
- 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.
Keywords:
- sRNA
- small RNA
- phasing
- phase-initiator
- sRNA cluster
- plant RNA
Literature & Tutorials:
This record last updated: 07-21-2008