Computational detection and analysis of sequences with duplex-derived interstrand G-quadruplex forming potential

► We present a new method for detection of DNA sequences with G-quadruplex forming potential, called ddiQFP. ► ddiQFP predicts G-quadruplexes formed from G-runs located on both strands of a DNA duplex. ► Yeast ddiQFP motifs distribute non-randomly, including in the nuclear vs. mitochondrial genomes. ► The G-quadruplex helicase Pif1 not only preferentially targets intramolecular QFP but also ddiQFP.