4.8 Article

A guide to computational methods for G-quadruplex prediction

Journal

NUCLEIC ACIDS RESEARCH
Volume 48, Issue 1, Pages 1-15

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/nar/gkz1097

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Funding

  1. PIC3i program from Institut Curie [91730]
  2. French Ministry of Education, Research and Technology

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Guanine-rich nucleic acids can fold into the non-B DNA or RNA structures called G-quadruplexes (G4). Recent methodological developments have allowed the characterization of specific G-quadruplex structures in vitro as well as in vivo, and at a much higher throughput, in silico, which has greatly expanded our understanding of G4-associated functions. Typically, the consensus motif G(3+)N(1-7)G(3+)N(1-7)G(3+)N(1-7)G(3+) has been used to identify potential G-quadruplexes from primary sequence. Since, various algorithms have been developed to predict the potential formation of quadruplexes directly from DNA or RNA sequences and the number of studies reporting genome-wide G4 exploration across species has rapidly increased. More recently, new methodologies have also appeared, proposing other estimates which consider non-canonical sequences and/or structure propensity and stability. The present review aims at providing an updated overview of the current open-source G-quadruplex prediction algorithms and straightforward examples of their implementation.

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