MicroRNAs (miRNAs) are small, non-protein coding RNAs (ncRNAs) with size about 22 nucleotides. They are increasingly recognized as important regulators of many processes in eukaryotic systems.

Empowered with the next generation sequencing technique, researchers are now able to comprehensively analyze miRNAs data.The sheer size of miRNAs data avaiable has generated sizable demand for computational tools to assist researchers in their miRNAs analysis pipeline. Here, we present "miRNA Workbench", a toolkit for miRNA identification and target prediction experiments.

The miRNA Workbench provides an integrated software environment that facilitates the process of systematic miRNAs data analysis. Starting with the raw input data in FastQ format, the miRNA Workbench pre-processes the input data by converting it into FastA format, and removing low-quality sequences. The analysis of miRNA data are divided into two main steps. The first step is the identification of known and novel miRNAs, and the second step is the miRNA target prediction. All these miRNAs data analysis tasks are tied together into a single workflow.

Another key feature of the miRNA Workbench is the customization of algorithms used in each of the analysis steps. With the apparent increases in the importance of miRNAs, we anticipate that many new algorithmic techniques for miRNAs data analysis will be developed in the near future. In this respect, the miRNA Workbench can be used by researchers to experiment with different algorithms for miRNA data analysis.