PinMol – Design Molecular Beacons for Imaging

The input file used by PinMol is the ss-count file obtained after running mfold (RNA form) to fold the mRNA target of interest.

The ss-count should be saved as ASCII/ANSI text file. PinMol will give an error if a formatted file is used (RTF, doc, etc.).

Requirements: python v 3.x, pandas < v 0.19, Biopython and RNAstructure text-interface.

PinMol Download Links on GitHub (text-based interface):

Win version

Mac version

Tutorial PinMol Mac

oskar-specific molecular beacons with 24 nt probe length – PinMol output files as zip

Coming soon: PinMol GUI (using Tkinter)