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psRNATarget: a plant small RNA target analysis server (2017 release)
Xinbin Dai1, Zhaohong Zhuang1, Patrick Xuechun Zhao1
1Bioinformatics and Computational Biology Lab, Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
Nucleic Acids Research
|May 3, 2018
Summary
The psRNATarget tool was updated to improve the identification of plant regulatory small RNAs (sRNAs) and their messenger RNA targets. Enhanced features increase accuracy and handle large datasets for better gene regulation research.
Area of Science:
- Plant molecular biology
- Genetics
- Bioinformatics
Background:
- Plant regulatory small RNAs (sRNAs), including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs), are crucial for gene expression regulation.
- These sRNAs utilize conserved mechanisms for post-translational gene silencing and translational inhibition.
- Accurate identification of sRNA targets is essential for understanding gene regulatory networks.
Purpose of the Study:
- To enhance the psRNATarget tool for more accurate and efficient identification of plant sRNA targets.
- To improve the analysis of miRNA-mRNA interactions with higher recall rates.
- To facilitate the analysis of large biological datasets through improved data handling and computing power.
Main Methods:
- Development of a new scoring schema for analyzing sRNA-mRNA sequence complementarity and target site accessibility.
- Implementation of multi-threading for chunked file uploading (HTML5 APIs) to support big data transmission.
- Allocation of additional computing nodes to the back-end Linux cluster for enhanced processing capabilities.
Main Results:
- The updated scoring schema significantly improves the discovery of miRNA-mRNA interactions at higher recall rates.
- The tool now efficiently handles and analyzes large 'big' data volumes.
- User interfaces have been refined for clarity, conciseness, and improved user experience.
Conclusions:
- The updated psRNATarget server provides a more powerful and user-friendly platform for plant sRNA target prediction.
- Enhanced analytical performance and data handling capabilities support advanced research in plant gene regulation.
- The freely available tool empowers researchers to investigate complex sRNA-mediated gene silencing pathways.
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