Primer PICKR: literature-mined scoring platform for robust RT–qPCR primers

Abstract

Abstract Reliable reverse-transcription quantitative PCR (RT–qPCR) depends on well-designed primers, yet undocumented or poorly validated sequences continue to compromise reproducibility. Existing resources catalog only modest sets of empirically verified primers or generate de-novo primer pairs without experimental validation. Here, we introduce Primer PICKR (Publication Integrations for Composite Knowledge Ranking), a large-scale, open, continuously updated database that systematically converts >7,000,000 community-validated oligonucleotides from >400,000 papers into actionable design resources. PICKR aligns sequences to reference transcriptomes and assembles ranked primer pairs for over 6000 genes across ten model organisms. Composite scoring integrates citation frequency, biophysical quality, and primer-pair synergy, while experimental validation of 154 human primer pairs spanning the score distribution demonstrates near-perfect amplification success above a PICKR score of 80. By converting decades of scattered primer choices into an immediately searchable database, Primer PICKR reduces empirical screening, conserves scarce samples, and accelerates reproducible assay development.