Computer-aided probability base calling for arrays of nucleic acid probes on chips
AssigneeAffymetrix, Inc.
InventorsRobert J. Lipshutz, Michael G. Walker
Life of this patent
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Abstract
A computer system for analyzing nucleic acid sequences is provided. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.
Claims29
In a computer system, a method of calling an unknown base in a sample nucleic acid sequence, the method comprising the steps of:
- inputting a plurality of hybridization probe intensities, each of the probe intensities corresponding to a nucleic acid probe;
- for each of the plurality of probe intensities, determining a probability that the corresponding nucleic acid probe best hybridizes with the sample nucleic acid sequence;
- and
- calling the unknown base according to the nucleic acid probe with the highest associated probability.
A computer program that calls an unknown base in a sample nucleic acid sequence, comprising:
- code that receives as input a plurality of hybridization probe intensities, each of the probe intensities corresponding to a nucleic acid probe;
- code that determines for each of the plurality of probe intensities a probability that the corresponding nucleic acid probe best hybridizes with the sample nucleic acid sequence;
- and
- code that calls the unknown base according to the nucleic acid probe with the highest associated probability;
- wherein the codes are stored on a tangible medium.
In a computer system, a method of calling an unknown base in a sample nucleic acid sequence, the method comprising the steps of:
- inputting a plurality of base calls for the unknown base, each of the base calls having an associated probability which represents a confidence that the unknown base is called correctly;
- selecting a base call that has a highest associated probability;
- and
- calling the unknown base according to the selected base call.
A computer program that calls an unknown base in a sample nucleic acid sequence, comprising:
- code that receives as input a plurality of base calls for the unknown base, each of the base calls having an associated probability which represents a confidence that the unknown base is called correctly;
- selecting a base call that has a highest associated probability;
- and
- calling the unknown base according to the selected base call;
- wherein the codes are stored on a tangible medium.
In a computer system, a method of calling an unknown base in a sample nucleic acid sequence, the method comprising the steps of:
- inputting a plurality of probabilities for each possible base for the unknown base, each of the probabilities representing a probability that the unknown base is an associated base;
- producing a product of probabilities for each possible base, each product being associated with a possible base;
- and
- calling the unknown base according to a base associated with a highest product.
A computer program that calls an unknown base in a sample nucleic acid sequence, comprising:
- code that receives as input a plurality of probabilities for each possible base for the unknown base, each of the probabilities representing a probability that the unknown base is an associated base;
- code that produces a product of probabilities for each possible base, each product being associated with a possible base;
- and
- code that calls the unknown base according to a base associated with a highest product;
- wherein the codes are stored on a tangible medium.
In a computer system, a method of calling an unknown base in a sample nucleic acid sequence, the method comprising the steps of:
- inputting a first base call for the unknown base, the first base call determined from a first nucleic acid probe that is equivalent to a portion of the sample nucleic acid sequence including the unknown base;
- inputting a second base call for the unknown base, the second base call determined from a second nucleic acid probe that is complementary to a portion of the sample nucleic acid sequence including the unknown base;
- selecting one of the first or second nucleic acid probes that has a base at an interrogation position which has a high probability of producing correct base calls;
- and
- calling the unknown base according to the selected one of the first or second nucleic acid probes.
A computer program that calls an unknown base in a sample nucleic acid sequence, comprising:
- code that receives as input first and second base calls for the unknown base, the first base call determined from a first nucleic acid probe that is equivalent to a portion of the sample nucleic acid sequence including the unknown base and the second base call determined from a second nucleic acid probe that is complementary to a portion of the sample nucleic acid sequence including the unknown base;
- code that selects one of the first or second nucleic acid probes that has a base at an interrogation position which has a high probability of producing correct base calls;
- and
- code that calls the unknown base according to the selected one of the first or second nucleic acid probes;
- wherein the codes are stored on a tangible medium.
Dependencies are inferred from the claim text.