SIROCCO Tools

Here is the set of tools which can be used to process data for silencing RNA. Unsure how to proceed? Try our getting started guide.

Small RNA Analysis

UEA plant small RNA toolkit

A toolkit for analysing large-scale plant small RNA datasets.

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Artificial microRNAs

WMD

WMD (Web MicroRNA Designer) is a web-tool for the automated design of artificial microRNAs. Currently on version 2, version 3 will be released soon.

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Short Read Sequencing

SHORE

SHORE is a tool for the analysis of Illumina Genome Analyzer expression data, including both mRNA sequencing (mRNA-seq) and small RNA sequencing (sRNA-seq). It includes preprocessing and quality filtering of Illumina GA reads, mapping of reads against a reference genome, splice site detection for mRNA-seq as well as quantitative expression analysis and visualization.

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Micro Arrays

Arabidopsis thaliana - Tiling Array Express (At-TAX)

At-TAX is a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana.
Tiling array hybridization intensities, probe set definitions for Arabidopsis genes and segmentations into exonic and background regions are visualized in a genome browser. Visualizations of gene expression and cross-platform comparisons are available through tileViz.

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