Publication Details
pqsfinder: imperfection-tolerant identification of potential quadruplex-forming sequences in R
Lexa Matej, Ing., Ph.D. (DCSY FIT BUT)
Martínek Tomáš, doc. Ing., Ph.D. (DCSY FIT BUT)
Zendulka Jaroslav, doc. Ing., CSc. (DIFS FIT BUT)
Motivation: G-quadruplexes (G4s) are one of the non-B DNA structures easily observed in vitro and suspected to form in vivo. Latest experiments with G4-specific antibodies and G4-unwinding helicase mutants confirm these suspicions. These four-stranded structures have also been shown to influence a range of molecular processes in cells. Because the structures are intensively studied, it is often desirable to screen DNA sequences and pinpoint the precise locations where G4s might form. With Bioconductor being a popular platform for sequence analysis, we were motivated to provide such search capability to its users, building on our previous research of triplex-forming sequence detection. In the newly presented approach, we allow for flexible searches that accommodate possible divergence from the optimal base composition. The existence of such imperfections was one of the main conclusions of the recently published G4-seq experiments.
Results: We describe a Bioconductor package for identifying potential quadruplex-forming sequences (PQS) that is easy-to-use but is at the same time also flexible and scalable. We demonstrate that the algorithm behind the searches has a 96% accuracy on 392 currently known and experimentally observed G4 structures. We also carried out searches against the recent G4-seq data to verify how well we can identify the structures detected by that technology. The correlation with pqsfinder predictions was 0.622, higher than the correlation obtained with the second best G4Hunter.