Journal
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Volume 10, Issue 4, Pages 832-844Publisher
IEEE COMPUTER SOC
DOI: 10.1109/TCBB.2013.7
Keywords
Dynamic programming; RNA folding; ViennaRNA Package
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Funding
- German Research Foundation [STA 850/7-2]
- Austrian GEN-AU
- Austrian FWF
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G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters, we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead. Stable G-quadruplexes are strongly enriched, however, in the 5'UTR of protein coding mRNAs.
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