doi: 10.1016/0022-5193(84)90029-8.
Structural and combinatorial constraints on base pairing in large nucleotide sequences
- PMID: 6201680
- DOI: 10.1016/0022-5193(84)90029-8
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Structural and combinatorial constraints on base pairing in large nucleotide sequences
J Theor Biol.
.
Abstract
In this paper we discuss the constraints and combinatorial problems of folding long RNA and single stranded DNA molecules into base paired structures. A computer code FOLD-A was designed to perform base pairing foldings of very long sequence chains and search for low energy configurations. The logic of the FOLD-A algorithm is described in some detail. The applications of FOLD-A to the A-protein gene of MS2 and the whole genome of the phi X 174 phage with over 5300 bases are discussed in the accompanying paper.
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