UMMS Affiliation

Department of Medicine, Division of Infectious Diseases and Immunology

Publication Date


Document Type



Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology | Computer Sciences | 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


Small interfering RNA, Oligonucleotides, RNA interference, Antisense oligonucleotides, RNA structure, Sequence alignment, Sequence motif analysis, Single nucleotide polymorphisms

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Copyright: © 2021 Sciabola et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

DOI of Published Version



Sciabola S, Xi H, Cruz D, Cao Q, Lawrence C, Zhang T, Rotstein S, Hughes JD, Caffrey DR, Stanton RV. PFRED: A computational platform for siRNA and antisense oligonucleotides design. PLoS One. 2021 Jan 22;16(1):e0238753. doi: 10.1371/journal.pone.0238753. PMID: 33481821; PMCID: PMC7822268. Link to article on publisher's site

Journal/Book/Conference Title

PloS one

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Link to Article in PubMed

PubMed ID


Creative Commons License

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