Welcome to the UEA sRNA toolkit

This site provides access to our software tools for the analysis of high-throughput small RNA data. This is the plant-specific version of the site. We also provide a version for animal datasets.
We will continue to add more tools and features to this site and we welcome your feedback to improve the tools.

We recently published a review on RNA silencing in plants, which discusses the computational analysis of large-scale sRNA datasets (link to article).

New: A Java based sRNA workbench is available for download currently containing a subset of the sRNA toolkit functionality.
It is available for download at the following location: srna-workbench.cmp.uea.ac.uk


Tools available:

Sequence file pre-processing: Sequence adaptor removal and conversion to FASTA format
Filter tool: Filter sequences in large-scale data sets
miRProf: Expression profiles of known miRNAs from large scale sRNA data sets
miRCat: Identification of miRNA sequences in large-scale sRNA data sets
Target prediction tool: Prediction of plant miRNA/ta-siRNA target sequences
FiRePat: identify regulatory patterns from gene ans sRNA expression data
SiLoCo: Identification and comparison of sRNA-producing loci in large-scale data sets
SiLoMa: Generate graphical maps of individual sRNA loci.
trans-acting siRNA prediction tool: Detection of phased siRNAs from large-scale sRNA sequence data
RNA folding/annotation: For highlighting sRNA locations on a folded RNA sequence.