G4-iM Grinder: DNA and RNA G-Quadruplex, i-Motif and higher order structure search and analyser tool

We present G4-iM Grinder as a system for potential quadruplex and higher-order quadruplex identification and characterization. Several grading tools of biological relevance and formation probability are included in this modulable and robust engine. G4-iM Grinder improves other quadruplex search engines in capabilities and processing time. We used G4-iM Grinder to analyse the complete human genome whilst focusing on frequency and PQS score. We studied the most recurrent potential quadruplex sequences (PQS) and the longest highest scoring potential higher order quadruplex sequences (PHOQS). As proof of the analytical capabilities of G4-iM Grinder, we also analysed a new PHOQS and predicted the most probable subunits to form it. Taking the human average PQS density as reference, we examined the genomes of organisms that cause leishmaniosis, diphtheria, brucellosis, meningitis, pneumonia, toxoplasmosis, tuberculosis, leprosy, AIDS, dengue fever and hepatitis C, and found they are rich in PQS. G4-iM Grinder identified within many of these several already known-to-form sequences. Together, this suggests that G-quadruplexes may potentially be important therapeutic targets against many of these organisms that currently kill millions worldwide.