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. 1988 Mar 11;16(5 Pt A):1703–1714. doi: 10.1093/nar/16.5.1703

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

M Dubnick 1, L K Lewis 1, D W Mount 1
PMCID: PMC338165  PMID: 3353219

Abstract

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 self-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.

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Selected References

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