Method for identifying suitable nucleic acid probe sequences for use in nucleic acid arrays
First Claim
1. A method of identifying candidate probe sequences for a nucleic acid sequence for use as probes in a nucleic acid array, said method comprising:
- (a) providing a set of known, undesirable probe sequences present in a format representative of the nucleotide sequences of said known, undesirable probe sequences, wherein said set of undesirable probe sequences comprises probe sequences that do not meet a predetermined specificity of binding affinity for said nucleic acid sequence;
(b) comparing said nucleic acid sequence present in a format representative of the nucleotide sequence of said nucleic acid sequence to each member of said set;
(c) marking regions of said nucleic acid sequence that have no more than 5 mismatches with a sequence of a member of said set as undesirable regions for candidate probe sequences for said nucleic acid sequence;
(d) identifying candidate probe sequences for said nucleic acid sequence for use as probes in a nucleic acid array from unmarked regions of said nucleic acid sequence; and
(e) synthesizing at least one of said identified candidate probe sequences.
1 Assignment
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Accused Products
Abstract
Methods of identifying regions of a nucleic acid sequence suitable for use as probes in nucleic acid arrays, as well as compositions of matter for practicing such methods, are provided. The subject methods include: (a) providing a set of known, undesirable probe sequences; (b) comparing a nucleic acid sequence to each member of the set; and (c) identifying regions of the nucleic acid sequence that substantially match a sequence of a member of the probe set as undesirable regions. The subject methods also include marking the undesirable regions of the nucleic acid sequence to identify regions of the nucleic acid sequence that are suitable for use as probes in a nucleic acid array. The subject invention also includes an algorithm and kits for carrying out the subject methods. Also provided are nucleic acid arrays produced with the identified suitable probes, and methods for using the same.
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Citations
40 Claims
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1. A method of identifying candidate probe sequences for a nucleic acid sequence for use as probes in a nucleic acid array, said method comprising:
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(a) providing a set of known, undesirable probe sequences present in a format representative of the nucleotide sequences of said known, undesirable probe sequences, wherein said set of undesirable probe sequences comprises probe sequences that do not meet a predetermined specificity of binding affinity for said nucleic acid sequence; (b) comparing said nucleic acid sequence present in a format representative of the nucleotide sequence of said nucleic acid sequence to each member of said set; (c) marking regions of said nucleic acid sequence that have no more than 5 mismatches with a sequence of a member of said set as undesirable regions for candidate probe sequences for said nucleic acid sequence; (d) identifying candidate probe sequences for said nucleic acid sequence for use as probes in a nucleic acid array from unmarked regions of said nucleic acid sequence; and (e) synthesizing at least one of said identified candidate probe sequences. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 35, 38)
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15. A method of identifying candidate probe sequences for a nucleic acid sequence for use as probes in a nucleic acid array, said method comprising:
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(a) providing a set of known, undesirable probe sequences present in a format representative of the nucleotide sequences of said known, undesirable probe sequences, wherein said set of undesirable probe sequences comprises probe sequence that do not meet a predetermined specificity of binding affinity for said nucleic acid sequence; (b) comparing said nucleic acid sequence present in a format representative of the nucleotide sequence of said nucleic acid sequence to each member of said set; and (c) marking regions of said nucleic acid sequence that have no more than 2 mismatches with a sequence of a member of said set as undesirable regions for candidate probe sequences for said nucleic acid sequence; (d) identifying candidate probe sequences for said nucleic acid sequence for use as probes in a nucleic acid array from unmarked regions of said nucleic acid sequence; and (e) synthesizing at least one of said identified candidate probe sequences. - View Dependent Claims (16, 17, 18, 19, 20, 21, 31, 32, 36, 39)
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22. A method of identifying candidate probe sequences for a nucleic acid sequence for use as probes in a nucleic acid array, said method comprising:
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(a) providing a set of known, undesirable probe sequences present in a format representative of the nucleotide sequences of said known, undesirable probe sequences, wherein said set of undesirable probe sequences comprises probe sequences that do not meet a predetermined specificity of binding affinity for said nucleic acid sequence; (b) comparing said nucleic acid sequence present in a format representative of the nucleotide sequence of said nucleic acid sequence to each member of said set; and (c) marking regions of said nucleic acid sequence that have no mismatches with a sequence of a member of said set as undesirable regions for candidate probe sequences for said nucleic acid sequence; (d) identifying candidate probe sequences for said nucleic acid sequence for use as probes in a nucleic acid array from unmarked regions of said nucleic acid sequence; and (e) synthesizing at least one of said identified candidate probe sequences. - View Dependent Claims (23, 24, 25, 26, 27, 28, 33, 34, 37, 40)
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Specification