Accurate identification of organisms based on individual information content
First Claim
1. A method for identification of an organism, comprising the steps of:
- a) aligning a set of related sequences, wherein said set of related sequences comprise at least one polynucleotide sequence from said organism;
b) searching for a segment with low average information content from said set of aligned related sequences;
c) selecting from said segment one or more sequences with low individual information contents or a portion thereof as oligonucleotides for identification of said organism; and
d) hybridizing said oligonucleotides with at least one DNA molecule obtained from said organism,wherein the average information content is determined by calculating and comparing the values of Rsequence for every equal-length window on said aligned sequences.
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Abstract
An improved method for specific identification of any organisms by DNA hybridization or amplification is disclosed. Oligonucleotides are designed based on information analysis of sequences from a large number of related species. Oligonucleotide sequences that have the maximal specificity to certain nucleic acids from a particular species (or set of species) or type strain are selected for hybridization or amplification using DNA from the target organism. The presence or absence of a PCR or hybridization product may be used to identify the target organism. The resulting PCR products may also be compared with a DNA sequence database to obtain the identity of the organisms. The methods may prove useful in areas where rapid and accurate identification of an organism is desirable, such as in a hospital where identification of infectious agents may be critical, in the ethanol or beer industry where certain bacteria may be detrimental to the manufacturing process, or in the porcine industry where identification of different type strains of the porcine reproductive and respiratory syndrome virus (PRRV) is important for disease prevention.
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Citations
20 Claims
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1. A method for identification of an organism, comprising the steps of:
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a) aligning a set of related sequences, wherein said set of related sequences comprise at least one polynucleotide sequence from said organism; b) searching for a segment with low average information content from said set of aligned related sequences; c) selecting from said segment one or more sequences with low individual information contents or a portion thereof as oligonucleotides for identification of said organism; and d) hybridizing said oligonucleotides with at least one DNA molecule obtained from said organism, wherein the average information content is determined by calculating and comparing the values of Rsequence for every equal-length window on said aligned sequences. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
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9. A method for identification of an organism, comprising the steps of:
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a) aligning a first polynucleotide sequence known to exist in a first organism with at least one additional related polynucleotide sequence from at least one different organism, said at least one additional related polynucleotide sequence being different from one another and from said first polynucleotide sequence; b) searching for a window with low average information content on said aligned sequences; c) selecting from said first polynucleotide sequence at least one segment with low individual information content or a portion thereof as an oligonucleotide for identification of said first organism; and d) hybridizing said oligonucleotides with at least one DNA molecule obtained from said organism, wherein the average information content is determined by calculating and comparing the values of Rsequence for every equal-length window on said aligned sequences. - View Dependent Claims (10, 11, 12, 13, 14, 15)
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16. A method for identification of a type strain, comprising the steps of:
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a) aligning a first polynucleotide sequence known to exist in a first type strain with at least one additional polynucleotide sequence from at least one different type strain, wherein said at least one additional polynucleotide sequence is different from one another and from said first polynucleotide sequence, and said first type strain and said at least one different type strain belong to the same species; b) searching for a window with low average information content on said aligned sequences; and c) selecting from said first polynucleotide sequence at least one segment with low individual information content or a portion thereof as an oligonucleotide for identification of said first type strain. - View Dependent Claims (17, 19)
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18. A method for identification of an organism, comprising the steps of:
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a) aligning a first polynucleotide sequence known to exist in a first organism with at least one additional related polynucleotide sequence from at least one different organism, said at least one additional polynucleotide sequence being different from one another and from said first polynucleotide sequence; b) searching for a window with low average information content on said aligned sequences, wherein the average information content is determined by calculating and comparing the values of Rsequence for every equal-length segment in the aligned sequences; and c) selecting from said first polynucleotide sequence at least one segment with low individual information content or a portion thereof as an oligonucleotide for identification of said first organism. - View Dependent Claims (20)
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Specification