UMass Chan Medical School Faculty Publications

UMMS Affiliation

Department of Medicine, Division of Infectious Diseases and Immunology

Publication Date


Document Type

Article Preprint


Bioinformatics | Computational Biology | Nucleic Acids, Nucleotides, and Nucleosides


PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at as a java Jar file. The source code and the links for downloading the precompiled version can be found at


bioinformatics, siRNA, antisense oligonucleotides, PFRED, open source, software platform

Rights and Permissions

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY 4.0 International license.

DOI of Published Version



bioRxiv 2020.08.25.265983; doi: Link to preprint on bioRxiv service.

Journal/Book/Conference Title


Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.