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生二乙 499432072 紀廷璇

The UEA sRNA Workbench: A Suite of Tools for Analysing and Visualising Next Generation Sequencing microRNA and Small RNA Datasets. 生資專題 討論 期末 報告. 生二乙 499432072 紀廷璇. INTRODUCTION ：. RNA silencing is a complex, highly conserved mechanism mediated by sRNAs .

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生二乙 499432072 紀廷璇

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  1. The UEA sRNA Workbench: A Suite of Tools forAnalysing and Visualising Next Generation SequencingmicroRNA and Small RNA Datasets 生資專題討論 期末報告 生二乙 499432072 紀廷璇

  2. INTRODUCTION： • RNA silencing is a complex, highly conserved mechanism mediated by sRNAs. • To better understand sRNA pathways, NGS technologies have become the de facto way to generate sRNA datasets. • Here we present the UEA sRNA Workbench, a suite of interactiveJava-based sRNA analysis tools, which provides an easy-to-use,well documented platform to create workflows for processings RNA NGS data.

  3. DESCRIPTION OF THE WORKBENCH

  4. 1. Helper Tools • Adaptor Remover • Filter produces • Sequence Alignment

  5. 2. Computational Analysis Tools • miRCat(miRNACategorisation) predicts mature miRNAs and theirprecursorsfrom an sRNA dataset and a genome. • SiLoCo (Short interfering RNA Locus Comparison) compares sRNAexpression levels by grouping sRNAs into loci based on genomic location . • ta-siRNA(trans-acting short interfering RNA) prediction is animplementationof an algorithm proposed in for prediction of phased ta-siRNAs in plant sRNA datasets. • miRProf (miRNA Profiler) determines normalised expression levelsofsRNAs matching known miRNAs in miRBase.

  6. 3.Visualisation Tools • Hairpin Annotation generates a secondary structure from an RNA sequence and highlights regions of interest using RNAplot.

  7. VisSR (Visualisation of sRNAs)Visualisation of sRNA features can be used to gain insight into their likely biogenesis or function. To do this VisSRutilises components from GenoViz to generate a visual representation of sRNAs and user-imported genomic features.

  8. DISCUSSION

  9. REFERENCES • The UEA sRNA Workbench: A Suite of Tools for Analysingand Visualising Next Generation Sequencing microRNA and Small RNA Datasets Matthew B. Stocks , Simon Moxon, Daniel Mapleson, Hugh C. Woolfenden, Irina Mohorianu, Leighton Folkes, Frank Schwach, TamasDalmay, Vincent Moulton ,Bioinformatics Advance Access published May 24, 2012

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