PFRED

Introduction

PFRED stands for Pfizer RNAi Enumeration and Design. PFRED is a client-server software system designed for selecting potent and specific siRNAs or RNase H-dependent antisense (ASO) agents. Highly effective sequences for post transcriptional gene regulation are chosen in PFRED using bioinformatics algorithms built upon careful mining of the sequence-activity relationships found in public datasets as well as internal collections. The tool provides researchers with a user friendly interface where the only required input is the gene ID information for the target being studied.  It returns a list of properties that might contribute to the effectiveness of an siRNA or ASO; these properties include human transcripts and cross-species homology, GC content, SNPs, intron-exon boundary, duplex thermodynamics, efficacy prediction score and off-target matches.  An automated oligonucleotide selection procedure is available in PFRED to quickly select one potential set of sequences with an appropriate property profile. The selection protocol can be customized by the user through changes of the selection cutoffs or the addition of alternate design parameters and algorithms

References

HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation. Tianhong Zhang*, Hongli Li, Simon Xi, Robert V. Stanton and Sergio H. Rotstein, J. Chem. Inf. Model., 2012, 52 (10), pp 2796–2806 Link to ACS Publications

PFRED: A Computational Tool for siRNA and Antisense Design. Simone Sciabola*, Hualin Xi, Dario Cruz, Qing Cao, Christine Lawrence, Tianhong Zhang, Sergio Rotstein, Jason D. Hughes, Daniel R. Caffrey, Robert V. Stanton, PLoS ONE 16(1): e0238753 Link to PLOS Publications