srnaworkbench

We have hosted the application srnaworkbench in order to run this application in our online workstations with Wine or directly.

Quick description about srnaworkbench:

A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data.

Features:

• 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 normalised 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

Audience: Science/Research.
User interface: Java Swing.
Programming Language: C++, Java.
Categories: