QPARSE is a Python program (Python v. 2.7) that allows to search for exact or degenerate putative patterns associated with the formation of four-stranded non-canonical nucleic-acids structures (quadruplex or PQS) and multimeric quadruplex structures [1, 2].
The tool can also assess the symmetrical properties of the linking loops to evaluate the potential of longer loops (>= 7 nt) to form hairpins that stabilize the quadruplex structure [2, 3].
QPARSE exploits an exhaustive graphs-based algorithm that allows to model all the possible PQS patterns considering all the combinations of islands that are detected based on the specified parameters.
Features:
- The tool can detect both exact or degenerate islands (i.e. islands containing any desired combination of bases and bulges, and mismatched islands).
- The tool can detect longer PQS with more than four consecutive islands that can potentially form multimeric quadruplexes.
- The tool is exhaustive in the search and all the possible combinations of the detected islands are considered.
- The tool can assess the symmetrical properties (mirror, palindromic or a combination of both) of the linking loops to evaluate the potential formation of hairpin structures that stabilize longer loops (>= 7 nt).
- The search is not limited to G or C but can be extended to any other base.
Publication: Michele Berselli, Enrico Lavezzo, Stefano Toppo, QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable, Bioinformatics, btz569, 10.1093/bioinformatics/btz569
References
[1] Characterization of G4–G4 Crosstalk in the c-KIT Promoter Region. Riccardo Rigo and Claudia Sissi. Biochemistry, 2017.
[2] Formation of a Unique End-to-End Stacked Pair of G-Quadruplexes in the hTERT Core Promoter with Implications for Inhibition of Telomerase by G-Quadruplex-Interactive Ligands. SunMi L. Palumbo, Scot W. Ebbinghaus, and Laurence H. Hurley. Journal of the American Chemical Society, 2009.
[3] Major G-Quadruplex Form of HIV-1 LTR Reveals a (3 + 1) Folding Topology Containing a Stem-Loop. Elena Butovskaya, Brahim Heddi, Blaž Bakalar, Sara N. Richter, and Anh Tuân Phan. Journal of the American Chemical Society, 2018.