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© Oxford University Press

On the application of integer arithmetic in nucleotide sequence analysis

D.A.Mac Dönaill

Department of Chemistry and Center for Scientific Compulation, Trinity College, University of Dublin Ireland

Email: dmcdonll{at}tcd.ie

A method exploiting quaternary integer arithmetic for the rapid comparison of nucleotide sequences is proposed. A central feature of the method is the identification of a suitable integer arithmetic operation which, operating on two numerical strings (representing two sequences), yields an output string unambiguously related to the number of matching nucleotides in the compared sequences. The number of matching nucleotide bases in compared sequences can be determined without having to make individual base by base comparisons. The method is a general extension of the algorithm previously described in the code UNIREP. The rules governing integer arithmetic as applied to nucleotide sequences are discussed.

Received on May 15, 1995; accepted on August 11, 1995

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