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...

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Bibliographic Details
Published in:Nucleic acids research 1988-03, Vol.16 (5), p.1703-1714
Main Authors: DUBNICK, M, LEWIS, L. K, MOUNT, D. W
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Animals
Base Sequence
Biological and medical sciences
Biotechnology
Codon
Computers
Diverse techniques
Fundamental and applied biological sciences. Psychology
Genetic engineering
Genetic technics
Humans
Methods. Procedures. Technologies
Microcomputers
Miscellaneous
Molecular and cellular biology
Nucleotide Mapping - methods
Oligonucleotides - genetics
Rats
Sequence Homology, Nucleic Acid
Software - methods
Synthetic digonucleotides and genes. Sequencing
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/16.5.1703