Probe design methods and microarrays for comparative genomic hybridization and location analysis
First Claim
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1. A computer-implemented method for generating a set of probe nucleic acid sequences, the method comprising:
- (a) sorting a plurality of candidate probe nucleic acid sequences, for a genomic region of interest, from smallest genomic distance to largest genomic distance between neighboring candidate probe nucleic acid sequences to produce a sorted plurality of candidate probe nucleic acid sequences;
(b) evaluating a probe parameter for a neighboring pair of candidate probe nucleic acid sequences from said sorted plurality to identify a first member of said neighboring pair with a more desirable probe parameter than a second pair member of said neighboring pair;
(c) removing said second pair member from said plurality;
(d) reiterating said sorting, evaluating and removing steps at least once to generate a set of probe nucleic acid sequences; and
(e) outputting said set of probe nucleic acid sequenceswherein said method is performed by a computer that is programmed to perform said method.
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Abstract
Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or comparative genome hybridization microarray, comprising selecting a plurality of potential target sequences, generating a plurality of candidate probes from the target sequences, filtering the plurality of candidate probes by analyzing candidate probes for selected probe properties in silico. Microarrays comprising probes selected by the methods of the invention are particularly useful for comparative genome hybridization and location analysis.
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Citations
20 Claims
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1. A computer-implemented method for generating a set of probe nucleic acid sequences, the method comprising:
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(a) sorting a plurality of candidate probe nucleic acid sequences, for a genomic region of interest, from smallest genomic distance to largest genomic distance between neighboring candidate probe nucleic acid sequences to produce a sorted plurality of candidate probe nucleic acid sequences; (b) evaluating a probe parameter for a neighboring pair of candidate probe nucleic acid sequences from said sorted plurality to identify a first member of said neighboring pair with a more desirable probe parameter than a second pair member of said neighboring pair; (c) removing said second pair member from said plurality; (d) reiterating said sorting, evaluating and removing steps at least once to generate a set of probe nucleic acid sequences; and (e) outputting said set of probe nucleic acid sequences wherein said method is performed by a computer that is programmed to perform said method. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A non-transitory computer readable medium comprising instructions for performing the following method:
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(a) sorting a plurality of candidate probe nucleic acid sequences, for a genomic region of interest, from smallest genomic distance to largest genomic distance between neighboring candidate probe nucleic acid sequences to produce a sorted plurality of candidate probe nucleic acid sequences; (b) evaluating a probe parameter for a neighboring pair of candidate probe nucleic acid sequences from said sorted plurality to identify a first member of said neighboring pair with a more desirable probe parameter than a second pair member of said neighboring pair; (c) removing said second pair member from said plurality; (d) reiterating said sorting, evaluating and removing steps at least once to generate a set of probe nucleic acid sequences; and (e) outputting said set of probe nucleic acid sequences. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20)
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Specification