Structural and combinatorial constraints on base pairing in large nucleotide sequences

Ruth Nussinov, George Pieczenik

Research output: Contribution to journalArticlepeer-review

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 φX 174 phage with over 5300 bases are discussed in the accompanying paper.

Original languageEnglish
Pages (from-to)245-259
Number of pages15
JournalJournal of Theoretical Biology
Volume106
Issue number3
DOIs
StatePublished - 7 Feb 1984
Externally publishedYes

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