BIGPROBE: a computer program that predicts the sequence of long oligonucleotide probes with high reliability.
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.
Dubnick
M
M
Department of Molecular and Cellular Biology, University of Arizona, Tucson 85721.
Lewis
L K
LK
Mount
D W
DW
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003062:Codon; D003201:Computers; D006801:Humans; D008838:Microcomputers; D009710:Nucleotide Mapping / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics*; D051381:Rats; D012689:Sequence Homology, Nucleic Acid; D012984:Software / Q000379:methods*
D003062:Codon; D009841:Oligonucleotides