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Nucleic Acids Research, 1983, Vol. 11, No. 13 4655-4663
© 1983

MOLECULAR BIOLOGY

Calculating the expected frequencies of potential secondary structure in nucleic acids as a function of stem length, loop size, base composition and nearest-neighbor frequencies

Walter M. Fitch

Department of Physiological Chemistry, University of Wisconsin-Madison Madison, WI 53706, USA

Received February 1, 1983. Revised June 3, 1983. Accepted June 3, 1983.

A formula is derived to estimate the expected frequency of potential secondary structure of a given stem length and loop size in a random sequence of nucleotides of known length and composition. An example 1s provided using the SV40 sequence which shows significant non-randomness in stem length but whose significance is reduced by more than six orders of magnitude by taking nearest neighbor frequencies into account.


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