METHODS FOR COMPUTING POSITIONAL BASE PROBABILITIES USING EXPERMINENTALS BASE VALUE DISTRIBUTIONS
First Claim
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1. A method for determining a relative base probability, comprising:
- a. providing experimental base values for a base at a position in a statistically significant set of target nucleic acids;
b. creating a distribution of said experimental base values;
c. determining a relative base probability of a base at a position of a target nucleic acid by comparing its experimental base value with the distribution of experimental base values.
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Abstract
Aspects of the various embodiments of the invention relate generally to computing relative base value probabilities using discrete experimental base values to calculate distributions of relative base probabilities. This information can be used with associated experimental measurements to increase the accuracy of the data analysis.
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Citations
25 Claims
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1. A method for determining a relative base probability, comprising:
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a. providing experimental base values for a base at a position in a statistically significant set of target nucleic acids; b. creating a distribution of said experimental base values; c. determining a relative base probability of a base at a position of a target nucleic acid by comparing its experimental base value with the distribution of experimental base values. - View Dependent Claims (2, 3, 4, 5, 12)
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6. The method of clam 1, wherein the base probability is determined using multiple experimental base values for one base for a position in the set of target nucleic acids.
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7. The method of clam 1, wherein the base probability is determined using multiple experimental base values for all bases for a position in the set of target nucleic acid.
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8. The method of clam 7, wherein the base probability is determined for each base for a position in a target nucleic acid.
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9. The method of clam 7, wherein four groups of four experimental base value distributions are created.
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10. The method of clam 8, wherein the distribution is characterized by clustering.
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11. The method of clam 8, wherein the base probabilities are determined for multiple positions in a target nucleic acid.
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13. A method for determining relative base probabilities, comprising:
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a. providing experimental base values for a base at a position in set of target nucleic acids; b. dividing said base values into two or more groups according to associated experimental measurements, wherein each group comprises a statistically significant number of experimental base values; c. creating a distribution of said bases values for each group of step (b); d. determining the relative base probability of a base in a position of a target nucleic in each group by comparing its experimental base value with the distribution of experimental base values in the relevant group. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20)
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21. A method of determining a relative base probability in a target nucleic acid, comprising the steps of:
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a. obtaining a plurality of experimental intensity base values at a position in a target nucleic acid; b. dividing the experimental intensity values into groups based on the identification of a second base in a target nucleic acid with a known position relative to the first base; c. creating an intensity value distribution for each group based on the plurality of base values obtained, wherein the groups comprise statistically significant number of experimental intensity values; and d. comparing the experimental intensity value of the first base to the distribution created from a relevant group to determine a relative base probability.
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22. A computer program for determining relative base probabilities, comprising:
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a. computer code that receives a plurality of signals corresponding to base values for a target nucleic acid; b. computer code for creating a distribution of said experimental base values; c. computer code for determining a relative base probability of a base at a position of the target nucleic acid by comparing its experimental base value with the distribution of experimental base values; and d. a computer readable medium that stores said computer codes. - View Dependent Claims (23)
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24. A system for determining relative base probabilities, comprising:
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a. a processor; and b. a computer readable medium coupled to said processor for storing a computer program comprising; i. computer code that receives a plurality of signals corresponding to a statistically significant number of experimental base values for a target nucleic acid; ii. computer code for creating a distribution of said experimental base values; and iii. computer code for determining a relative base probability of a base at a position of the target nucleic acid by comparing its experimental base value with the distribution of experimental base values. - View Dependent Claims (25)
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Specification