Methods for evaluating oligonucleotide probe sequences

• US 20050027461A1
• Filed: 06/24/2004
• Published: 02/03/2005
• Est. Priority Date: 02/10/1998
• Status: Abandoned Application

• Current Assignee: Glenda C. Delenstarr, Karen W. Shannon, Paul K. Wolber, Peter G. Webb, Robert H. Kincaid
• Original Assignee: Glenda C. Delenstarr, Karen W. Shannon, Paul K. Wolber, Peter G. Webb, Robert H. Kincaid
• Inventors: Kincaid, Robert H., Delenstarr, Glenda C., Shannon, Karen W., Wolber, Paul K., Webb, Peter G.
• Application Number:
  US10/877,231
• Publication Number:
  US 20050027461A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
• 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

Abstract

Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.

Claims

1. A method for producing an array comprising:

receiving one or more target polynucleotide sequences;

determining an evaluated probe set for each of said one or more target polynucleotide sequences;

outputting data relating to the oligonucleotide sequences of said evaulated probe set for each of said one or more target polynucleotide sequences; and

fabricating an array from said outputted data.

2. A method for producing an array comprising:

eceiving one or more target polynucleotide sequences;

determining an evaluated probe set for each of said one or more target polynucleotide sequences;

outputting data relating to the oligonucleotide sequences of said evaluated probe set for each of said one or more target polynucleotide sequences to a user for examination and modification, as desired to produce a final output data set; and

fabricating an array from said final output data set.

3. The method according to claim 2, wherein said array is useful in diagnostic applications.

4. The method according to claim 2, wherein said method comprises coummunicating said outputted data with another computer.

5. The method according to claim 2, wherein each of said evaulated probe sets is made up of probes evaulated for at least one parameter predictive of hybridization.

6. The method according to claim 2, wherein said array comprises nucleic acids synthesized on a support.

7. A system for fabricating an array, said system comprising:

an input device for receiving one or more target polynucleotide sequences;

a means for determining an evaluated probe set for each of said one or more target polynucleotide sequences;

a communication means for outputting data relating to the oligonucleotide sequences of said evaluated probe set for each of said one or more target polynucleotide sequences to a user for examination and modification, as desired to produce a final output data set; and

means for fabricating an array from said final output data set.

8. The system according to claim 7, wherein said communication means communicates with another computer.

9. The system according to claim 7, wherein said means for determining evaluated probe sets evaluates probes for at least one parameter predictive of hybridization.

10. The system according to claim 7, wherein said array comprises nucleic acids synthesized on a support.

11. A method for providing custom probe arrays, comprising the acts of:

receiving a user selection of one or more probe set identifiers that each identify a plurality of potential probes;

determining verified probe sets of verified probes corresponding to the probe set identifiers;

generating a custom probe array design based, at least in part, upon the verified probe sets; and

providing to the user one or more probe arrays based on the probe array design.

12. A method for providing custom probe arrays, comprising the acts of:

receiving a user selection of one or more probe set identifiers that identify one or more potential probes;

determining verified probe sets of verified probes corresponding to the probe set identifiers;

generating a custom probe array design based, at least in part, upon the verified probe sets;

enabling for display to the user a representation of one or more aspects of the custom probe array design via one or more graphical user interfaces enabled to receive a user selection specifying acceptance, modification, or rejection of the custom probe array design; and

providing to the user one or more probe arrays based on the probe array design and responsive to the user specification of acceptance or modification.

13. The method of claim 12, wherein:

one or more of the probe arrays is constructed and arranged to diagnose a disease or medical condition.

14. The method of claim 12, wherein:

the user selection is received over the Internet.

15. The method of claim 12, wherein:

the probe set identifiers comprise sequence information.

16. The method of claim 12, wherein:

the verified probe sets are determined based, at least in part, on any one or any combination of frequency, length, or position of probe sequence repeats;

probe sequence length, thermodynamic properties, energetic parameters, or uniqueness;

or one or more characteristics of target molecules specified by the user for use with the probe array.

17. The method of claim 12, wherein:

the graphical user interface is provided over a network.

18. The method of claim 5, wherein:

the probe arrays include synthesized or spotted probe arrays.

19. A system for providing custom probe arrays, comprising:

an input manager constructed and arranged to receive a user selection of one or more probe set identifiers that identify one or more potential probes;

a gene or EST verifier constructed and arranged to determine one or more verified probe sets of verified probes corresponding to the probe set identifiers;

a probe array generator constructed and arranged to generate a custom probe array design based, at least in part, upon the verified probe sets; and

a user data processor constructed and arranged to enable for display a representation of one or more aspects of the custom probe array design via one or more graphical user interfaces that are further enabled to receive a user selection specifying acceptance, modification, or rejection of the custom probe array design, and further is constructed and arranged to provide to the user one or more probe arrays based on a user selection specifying acceptance or modification of the probe array design.

20. The system of claim 19, wherein:

the user selection is received over the Internet.

21. The system of claim 19, wherein:

the probe set identifiers comprise sequence information.

22. The system of claim 19, wherein:

the verified probe sets are determined based, at least in part, on any one or any combination of frequency, length, or position of probe sequence repeats;

probe sequence length, thermodynamic properties, energetic parameters, or uniqueness;

or one or more characteristics of target molecules specified by the user for use with the probe array.

23. The system of claim 19, wherein:

the graphical user interface is provided over a network.

24. The system of claim 19, wherein:

the probe arrays include synthesized or spotted probe arrays.