Journal Article

PFRED: A computational platform for siRNA and antisense oligonucleotides design

Lawrence, Christine, Sciabola, Simone, Xi, Hualin, Stanton, Robert V., Rotstein, Sergio, Cao, Qing, Hughes, Jason D., Caffrey, Daniel R., Cruz, Dario, Zhang, Tianhong

2021

Overview

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 .

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Algorithms / Alternative splicing / Antisense oligonucleotides / Antisense RNA / Biology and life sciences / Chemical modification / Chemistry / Complementarity / Computational biology / Computational Biology - methods / Computer applications / Data warehouses / Design / DNA Primers - genetics / Enumeration / FDA approval / Gene Library / Genetic research / Genomics / Graphical user interface / Id protein / Java / Modules / Nucleotides / Oligonucleotides / Oligonucleotides - genetics / Oligonucleotides, Antisense - genetics / Pharmaceutical sciences / Properties / Protein structure / Research and Analysis Methods / Ribonuclease H / RNA, Small Interfering - genetics / RNA-mediated interference / Secondary structure / Single-nucleotide polymorphism / siRNA / Software / User interface / User-Computer Interface