Scope & Purpose

Prime editing enables precise nucleotide-level genome modifications without inducing double-strand breaks. The technology depends on a carefully engineered guide RNA — the pegRNA — whose secondary structure, primer-binding site (PBS), reverse-transcription (RT) template, and 3' protective elements all must be tuned for the target locus. PROpeg removes that tuning burden:

Generates plant-optimized pegRNA candidates from a wildtype-vs-edited sequence pair.
Ranks candidates against PAM, GC, T_m, and PE-window constraints in one pass.
Predicts in-vivo editing efficiency.
Computes optimal nucleotide linkers for engineered designs.
Renders secondary-structure views for every variant in the browser.

Designed for plants: Default scaffold sequences, primer presets (OsU3, TaU3, TaU6, pHn-Cas9-V2), and codon-usage tables target monocot and dicot crops. The same algorithms work on any eukaryotic locus, but the defaults assume a plant-editing context.

Developed By

ICAR — Central Rice Research Institute (CRRI), Cuttack

ICAR — Indian Agricultural Statistics Research Institute (IASRI), New Delhi

Released under the MIT License. Bundled third-party tools retain their original licenses (pegLIT — BSD 3-Clause, PRIDICT2 — MIT); the PE3/PE3b nicking logic is derived from pegFinder — MIT.