Computational approaches to the detection and analysis of sequences with intramolecular G-quadruplex forming potential.

Paul Ryvkin, Steve G Hershman, Li-San Wang, F Brad Johnson

Department of Pathology, Penn Center for Bioinformatics, and Graduate Group in Genomics and Computational Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.

Methods in molecular biology (Clifton, N.J.) 2010

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Sequences with the potential to form intramolecular G-quadruplexes (G4-structures) are found in highly nonrandom distributions in the genomes of diverse organisms. These sequences are associated with nucleic acid metabolic processes ranging from transcription and translation to recombination and telomere function. Here we review different computational methods for identifying potential G4-forming sequences and provide protocols for their implementation. We also discuss methods for assessing the significance and specificity of associations between the sequences and different biological functions.

Citation

Paul Ryvkin, Steve G Hershman, Li-San Wang, F Brad Johnson. Computational approaches to the detection and analysis of sequences with intramolecular G-quadruplex forming potential. Methods in molecular biology (Clifton, N.J.). 2010;608:39-50