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Nucleic Acids Research, 1988, Vol. 16, No. 5 1703-1714
© 1988

Articles

BIGPROBE: a computer program that predicts the sequence of long oligonucleotide probes with high reliability*

Mark Dubnik, L.Kevin Lewis and David W. Mount

Department of Molecular and Cellular Biology, University of Arizona Tucson, AZ 85721, USA

Received August 17, 1987. Revised October 23, 1987. Accepted October 23, 1987.

We have written a computer program, BIGPROBE, which facilitates the design of long nucleic acid probes from the partial or complete amino acid sequence of a protein. BIGPROBE relies upon information on codon usage, intercodon dinucleotide frequency, and potential probe seif-complementarity. We have examined the accuracy with which the program predicts coding sequences using sample human and rat genes and probe lengths of 30–60 nucleotides. Rat probe sequences selected by BIGPROBE using either codon usage or dinucleotide frequency data alone averaged 86–92% homology with the known exons of the corresponding gene sequences. Predictive accuracy with rat gene probes could be improved to 89–94%, depending upon probe length, by applying codon usage and dinucleotide frequency data in combination. Similar accuracy was achieved for human genes.

* Program availability: BIGPROBE is available for a nominal charge as an executable program on an IBM compatible disket from the Genetics Software Center, Biosciences West 308, Dept. of Mol. and Cell. Biol., Univ. of Arizona, Tucson, Az., 85721.


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