BIGPROBE: a Computer Program That Predicts the Sequence of Long Oligonucleotide Probes with High Reliability

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1988 Mar 11

PMID 3353219

Citations 1

Authors

M Dubnick

L K Lewis

D W Mount

Affiliations

Soon will be listed here.

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.

Citing Articles

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Han J, Lu C, Brown G, Rado T Proc Natl Acad Sci U S A. 1991; 88(2):335-9.

PMID: 1846440 PMC: 50805. DOI: 10.1073/pnas.88.2.335.

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