PFRED: A computational platform for siRNA and antisense oligonucleotides design
Authors
Sciabola, SimoneXi, Hualin
Cruz, Dario
Cao, Qing
Lawrence, Christine
Zhang, Tianhong
Rotstein, Sergio
Hughes, Jason D.
Caffrey, Daniel R.
Stanton, Robert V.
UMass Chan Affiliations
Department of Medicine, Division of Infectious Diseases and ImmunologyDocument Type
Journal ArticlePublication Date
2021-01-22Keywords
Small interfering RNAOligonucleotides
RNA interference
Antisense oligonucleotides
RNA structure
Sequence alignment
Sequence motif analysis
Single nucleotide polymorphisms
Biochemistry, Biophysics, and Structural Biology
Bioinformatics
Computational Biology
Computer Sciences
Nucleic Acids, Nucleotides, and Nucleosides
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Show full item recordAbstract
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 https://github.com/pfred/pfred-gui/releases/tag/v1.0 as a java Jar file. The source code and the links for downloading the precompiled version can be found at https://github.com/pfred.Source
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
DOI
10.1371/journal.pone.0238753Permanent Link to this Item
http://hdl.handle.net/20.500.14038/41768PubMed ID
33481821Related Resources
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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.Distribution License
http://creativecommons.org/licenses/by/4.0/ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0238753
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Except where otherwise noted, this item's license is described as 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.