All posts by small RNA Workbench

The Small RNA Workbench Version 4.5

The small RNA Workbench Version 4.5 ALPHA: Released: 02/05/2018

This release is the next Alpha release of the latest version of the UEA sRNA Workbench, Version 4. Please check out the frequently encountered problems for a list of known issues.

This version has two Java binaries. The first, ‘Workbench.jar’, is the standard binary for running the Workbench using the graphical user interface or through the command line. The second, ‘ServerWorkbench.jar’, is a version that can only run through the command line but does not require any JavaFX dependencies. This second version should hopefully resolve many problems regarding servers and machines that do not have the required libraries for JavaFX.

We highly recommend using the latest version of the Java 8.

This release contains the Alpha build for our latest workflow tool PAREsnip2, a much faster version of miRCat2, and a new version of FiRePat.



A new degradome analysis tool has been released in this version of the workbench. More information about this tool can be found here. PAREsnip2 is able to efficiently predict small RNA targets evidenced through degradome sequencing on a genome-wide scale using a configurable set of targeting rules. More information can be found here.

miRCat2 changes

As of version 4.5 of the Small RNA Workbench, we have included a much faster version of miRCat2 known as the ‘standalone’ version. This was developed as some users experienced long waits to obtain results due to the low memory database feature. Therefore, if you have the memory (RAM) available and you are running miRCat2 from the command-line, we recommend using the standalone version.

miRCat2 standalone version does exactly the same as the standard miRCat2 workflow, i.e. same input, output, and algorithm. The only difference in this version is that it does not use the Workbench database, it relies on the personal machine memory. It only works through the command-line, and to use it add the flag “-standalone” to the command-line parameters.

You can run miRCat2 standalone through the command-line using the following command:

java -jar Workbench.jar -tool mircat2 -config configFile.json [-standalone]


In this version we have included an updated FiRePat workflow. FiRePat (Finding Regulatory Patterns) is an unsupervised data mining tool for detecting sRNA-gene pairs with correlated expression levels. FiRePat is suitable for both animal and plant data. More information can be found here.