The UEA sRNA Workbench is a suite of tools for analyzing small RNA (sRNA) data from Next Generation Sequencing devices. This includes expression profiling of known micro RNA (miRNA), identification of novel miRNA in deep-sequencing data, and identification of other interesting landmarks within high-throughput genetic data. Version 4.7.1 Alpha is now available for download:
- Adaptor Remover: removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.
- Filter: produces a filtered version of an sRNA dataset, controlled by several user-defined criteria, including sequence length, abundance, complexity, transfer and ribosomal RNA removal.
- miRCat2 (miRNA Categorisation): predicts mature miRNAs and their precursors from an sRNA dataset and a genome.
- SiLoCo (Short interfering RNA Locus Comparison): compares sRNA expression levels in multiple samples by grouping sRNAs into loci based on genomic location
- ta-siRNA (trans-acting short interfering RNA): prediction of phased ta-siRNAs in plant sRNA datasets.
- miRProf (miRNA Profiler): determines normalized expression levels of sRNAs matching known miRNAs in miRBase.
- Hairpin Annotation: generates a secondary structure from an RNA sequence and highlights regions of interest using RNAplot
- VisSR (Visualisation of sRNAs): generate a visual representation of sRNAs and user-imported genomic features.
- PAREsnip2: Identify miRNA targets evidenced through the degradome.
Here is more information about a previous version: The UEA Small RNA Workbench Version 4.4.
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