ArticleNucleic acids research2008
pssRNAMiner: a plant short small RNA regulatory cascade analysis server.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 35 citations in OpenAlex.
- Role of non-coding RNAs in quality improvement of horticultural crops: computational tools, databases, and algorithms for identification and analysis.Functional & integrative genomics · 2025Review
- Genome-Wide Identification and Characterization of the Laccase Gene Family inPlants (Basel, Switzerland) · 2024Article
- Role of phasiRNAs in plant-pathogen interactions: molecular perspectives and bioinformatics tools.Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Review
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- PhasiRNAnalyzer: an integrated analyser for plant phased siRNAs.RNA biology · 2021Article
- Article
- MicroRNAs inGenes · 2019Article
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- Genome-Wide Identification of the LAC Gene Family and Its Expression Analysis Under Stress inMolecules (Basel, Switzerland) · 2019Article
- A comprehensive review of web-based resources of non-coding RNAs for plant science research.International journal of biological sciences · 2018Review
- HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks.Plant & cell physiology · 2016Article
- Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods.International journal of molecular sciences · 2015Review
- Article
- Article
- Differential RNAi responses of Nicotiana benthamiana individuals transformed with a hairpin-inducing construct during Plum pox virus challenge.Virus genes · 2014Article
- Cascading cis-cleavage on transcript from trans-acting siRNA-producing locus 3.International journal of molecular sciences · 2013Article
- An efficient algorithm for systematic analysis of nucleotide strings suitable for siRNA design.BMC research notes · 2011Article
- Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives.Frontiers in plant science · 2011Article
- Article
- MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.