Electronic hybridization assay and sequence analysis

• US 6,912,469 B1
• Filed: 05/01/2001
• Issued: 06/28/2005
• Est. Priority Date: 05/05/2000
• Status: Expired due to Fees

• Current Assignee: Kenneth J. Cool
• Original Assignee: Kenneth J. Cool
• Inventors: Cool, Kenneth J.
• Primary Examiner(s): Brusca, John S.
• Application Number:
  US09/846,985
• Time in Patent Office: 1,519 Days
• Field of Search: 702/19, 364/94, 700/1
• US Class Current: 702/19
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR

Abstract

An electronic hybridization assay implements a hybridization reaction, or a sequence analysis, on sequences representative of the sequences of the molecules under examination to provide an output representative of a chemical hybridization reaction. An electronic hybridization machine implements a correlation algorithm where the correlation output provides information regarding the relationship between the molecules under examination. In one aspect, the degree of similarity between the molecules is indicated by the correlation output value. In another aspect, a locus of similarity between the molecules is indicated by a maximum value in the correlation output sequence. In a particular aspect, the sequences are encoded in an optimized format to optimize the operation of the operation of the electronic hybridization machine.

Claims

1. A method, comprising:

executing an electronic hybridization assay on a first sequence and a reference sequence, the first sequence representing at least one or more subunits of a first molecule and the reference sequence representing at least one or more subunits of a second molecule;

providing an output representative of a hybridization reaction between the first and second molecules; and

encoding the first sequence so that said executing step is optimized, wherein the first sequence includes at least one positive value and at least one negative value.

2. A method as claimed in claim 1, said executing step including the step of performing a correlation algorithm on the first sequence and the reference sequence, the output of said providing step including a correlation output.

3. A method as claimed in claim 1, further including the step of identifying a first molecule based upon the output of said providing step.

4. A method as claimed in claim 1, further including the step of identifying a position of sequence similarity between the first molecule and the second molecule.

5. An apparatus, comprising:

means for executing an electronic hybridization assay on a first sequence and a reference sequence, the first sequence representing at least one or more subunits of a first molecule and the reference sequence representing at least one or more subunits of a second molecule;

means for providing an output representative of a hybridization reaction between the first and second molecules; and

means for encoding the first sequence so that execution by said executing means is optimized, wherein the first sequence includes at least one positive value and at least one negative value.

6. An apparatus as claimed in claim 5, said executing means comprising an electronic hybridization machine.

7. An apparatus as claimed in claim 5, said executing means comprising a computer appliance structure.

8. An apparatus as claimed in claim 5, said executing means comprising a digital signal processor structure.

9. An apparatus as claimed in claim 5, said executing means comprising a hardware correlator device structure.

10. An apparatus as claimed in claim 5, further comprising means for encoding the first sequence so that execution by said executing means is optimized.

11. An apparatus as claimed in claim 5, said executing means including means for performing a correlation algorithm on the first sequence and the reference sequence, the output of said providing means including a correlation output.

12. An apparatus as claimed in claim 5, further including means for identifying the first molecule based upon the output of said providing means.

13. An apparatus as claimed in claim 5, further including the means for identifying a position of sequence similarity between the first molecule and the second molecule.

14. A machine readable medium having a program of instructions stored thereon, the program of instructions for causing a machine to implement steps for executing an electronic hybridization assay according to the program of instructions, the steps comprising:

executing an electronic hybridization assay on a first sequence and a reference sequence, the first sequence representing at least one or more subunits of a first molecule and the reference sequence representing at least one or more subunits of a second molecule;

providing an output representative of a hybridization reaction between the first and second molecules; and

encoding the first sequence so that said executing step is optimized, wherein the first sequence includes at least one positive value and at least one negative value.

15. A machine readable medium as claimed in claim 14, further comprising the step of encoding the first sequence so that said executing step is optimized.

16. A machine readable medium as claimed in claim 14, the executing step including the step of performing a correlation algorithm on the first sequence and the reference sequence, the output of said providing step including a correlation output.