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A guide to computational methods for G-quadruplex prediction.

Emilia Puig Lombardi1, Arturo Londoño-Vallejo1

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Guanine-quadruplexes (G4) are non-B DNA/RNA structures. This review overviews current open-source G4 prediction algorithms, aiding genome-wide G4 exploration and understanding their functions.

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Area of Science:

  • Genomics and Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Guanine-rich nucleic acids form non-B DNA/RNA structures known as G-quadruplexes (G4).
  • Advancements in characterization (in vitro, in vivo, in silico) have expanded G4 function understanding.
  • Traditional G4 motif identification (G3+N1-7G3+N1-7G3+N1-7G3+) is being augmented by advanced algorithms.

Purpose of the Study:

  • To provide an updated overview of open-source G-quadruplex prediction algorithms.
  • To present straightforward examples of G4 algorithm implementation.
  • To facilitate genome-wide exploration of G4 structures across species.

Main Methods:

  • Review of existing and newly developed G-quadruplex prediction algorithms.
  • Analysis of methodologies considering canonical and non-canonical G4 sequences.
  • Inclusion of approaches evaluating G4 structure propensity and stability.

Main Results:

  • Identification and categorization of current open-source G4 prediction tools.
  • Demonstration of practical implementation of selected G4 prediction algorithms.
  • Highlighting the increasing number of genome-wide G4 exploration studies.

Conclusions:

  • The landscape of G-quadruplex prediction algorithms is rapidly evolving.
  • Open-source tools offer accessible means for G4 identification and analysis.
  • Continued development of prediction methodologies is crucial for advancing G4 research.