Structural and combinatorial constraints on base pairing in large nucleotide sequences.

R Nussinov; G Pieczenik

doi:10.1016/0022-5193(84)90029-8

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Structural and combinatorial constraints on base pairing in large nucleotide sequences.

R Nussinov·G Pieczenik

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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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Base Composition Base Sequence Computers DNA, Single-Stranded Models, Chemical Nucleic Acid Conformation RNA RNA, Messenger RNA, Transfer Journal Article Research Support, U.S. Gov't, P.H.S.

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R Nussinov, G Pieczenik. 1984-02-07. Structural and combinatorial constraints on base pairing in large nucleotide sequences.. https://doi.org/10.1016/0022-5193(84)90029-8

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