Abstract
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.
MeSH terms
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Algorithms
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Computational Biology / methods*
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DNA Primers / genetics*
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Gene Library
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Genomics
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Oligonucleotides / genetics
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Oligonucleotides, Antisense / genetics*
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RNA, Small Interfering / genetics
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Software
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User-Computer Interface
Substances
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DNA Primers
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Oligonucleotides
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Oligonucleotides, Antisense
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RNA, Small Interfering
Grants and funding
Several authors have commercial affiliations: SS is affiliated with Biogen Inc. HX is affiliated with Rgenta. QC is affiliated with Ra Pharmaceuticals. CL, TZ, SR, and RVS are affiliated with Pfizer. JDH is affiliated with Foundation Medicine. These companies provided funding in the form of salaries for all authors but did not have any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the "author contributions" section.