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Journal Articles Nucleic Acids Research Year : 2020

A guide to computational methods for G-quadruplex prediction

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Abstract

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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hal-03014352 , version 1 (19-11-2020)

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Emilia Puig lombardi, Arturo Londoño-Vallejo. A guide to computational methods for G-quadruplex prediction. Nucleic Acids Research, 2020, 48, pp.1 - 15. ⟨10.1093/nar/gkz1097⟩. ⟨hal-03014352⟩
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