Method and system for predicting nucleic acid hybridization thermodynamics and computer-readable storage medium for use therein
First Claim
1. A method for predicting nucleic acid hybridization thermodynamics, the method comprising:
- providing a database of thermodynamics parameters;
receiving hybridization information which represents at least one sequence;
receiving correction data;
receiving a first set of data which represents hybridization conditions; and
calculating hybridization thermodynamics including net hybridization thermodynamics based on the hybridization information, the thermodynamic parameters, the correction data and the first set of data.
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Abstract
Method and system to predict and optimize probe-target hybridization are provided. The method may be implemented using six interactive, interrelated, software modules. Module 1 predicts the hybridization thermodynamics of a duplex given the two strands. Module 2 finds the best primer of a given length binding to a given target. Module 3 executes a primer walk to find alternative binding sites of a given primer on a given target. Module 5 is a combination of Modules 2 and 3. Module 6 finds the alternative binding sites of a given primer on a given target (Module 3) and calculates the concentration of target with primer bound at primary and alternative sites. Module 7 is a combination of Modules 2 and 5 and also calculates the various concentrations. The six modules can be operated either through an interactive user interface or using batch file submission as provided by Module 4. The program is suited to predict DNA/DNA, RNA/RNA, and RNA/DNA systems.
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Citations
60 Claims
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1. A method for predicting nucleic acid hybridization thermodynamics, the method comprising:
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providing a database of thermodynamics parameters;
receiving hybridization information which represents at least one sequence;
receiving correction data;
receiving a first set of data which represents hybridization conditions; and
calculating hybridization thermodynamics including net hybridization thermodynamics based on the hybridization information, the thermodynamic parameters, the correction data and the first set of data. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)
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21. A system for predicting nucleic acid hybridization thermodynamics, the system comprising:
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a database of thermodynamics parameters;
means for receiving hybridization information which represents at least one sequence;
means for receiving correction data;
receiving a first set of data which represents hybridization conditions; and
means for calculating hybridization thermodynamics including net hybridization thermodynamics based on the hybridization information, the thermodynamic parameters, the correction data and the first set of data. - View Dependent Claims (22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40)
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41. A computer-readable storage medium having stored therein a database of thermodynamics parameters and a computer program which executes the steps of:
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receiving hybridization information which represents at least one sequence;
receiving correction data;
receiving a first set of data which represents hybridization conditions; and
calculating hybridization thermodynamics including net hybridization thermodynamics based on the hybridization information, the thermodynamic parameters, the correction data and the first set of data. - View Dependent Claims (42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60)
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Specification