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

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.

Direct amplification of a single dissected chromosomal segment by polymerase chain reaction: a human brain sodium channel gene is on chromosome 2q22-q23.

“…Two oligonucleotide primers (NaCh 6, 5'-AACTCCATGATCTGCCTGTT-3'; and NaCh 7A, 5'-ATGTACATGTTCACCACCAC-3') were constructed based on the hypothesis that known sodium channel gene sequences exhibiting high interspecies homology and conservation would also be represented in the human sodium channel gene. The final sequence of the primers was chosen from a group of degenerate sequences with the aid of the BIG PROBE computer program, which takes into account species preferences in codon usage (18). NaCh 6 and NaCh 7A were then used to prime PCRs using human genomic DNA as the template.…”

“…Primers referred to in the text are indicated by lines with arrows marking the 3' end. Oligonucleotides NaCh 6 and NaCh 7A were designed by using the program BIG PROBE (18), so it may or may not represent the true sequences of the gene in these regions. The nested primers NaCh 11 and NaCh 12 were synthesized directly from human sequence.…”

Development of a biotinylated DNA probe for detection and identification of infectious hematopoietic necrosis virus

“…The optimal 30-base sequence for a probe designed to hybridize to the messenger RNA of the nucleocapsid (N) gene was chosen using the Big Probe software package (Dubnick et al 1988) and the published N gene sequence of the Round Butte Hatchery isolate of IHNV (Gilmore & Leong 1988). The site selected was near the middle of the mRNA n~olecule, from nucleotides 427 to 456 (sense orientation) of the open reading frame.…”