Methods designing multiple mRNA transcript nucleic acid probe sequences for use in nucleic acid arrays
First Claim
1. A method of identifying a sequence of a nucleic acid that is suitable for use as a substrate surface immobilized probe that can hybridize to two or more different target nucleic acids that correspond to the same genomic coding sequence, said method comprising:
- (a) selecting at least one consensus sequence for two or more different mRNA transcripts that are transcribed from said same genomic coding sequence, wherein said two or more transcripts may or may not comprise all the known transcripts from said same genomic coding sequence; and
(b) choosing a probe sequence for said at least one consensus sequence to identify said suitable nucleic acid sequence.
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Abstract
Methods of identifying a sequence of a nucleic acid that is suitable for use as a surface immobilized probe for two or more mRNA transcripts encoded by the same gene are provided. In practicing the subject methods, a consensus region for the two or more transcripts is first identified, and this identified consensus region is then employed to identify the suitable nucleic acid sequence, e.g., by using a probe design protocol. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.
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Citations
19 Claims
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1. A method of identifying a sequence of a nucleic acid that is suitable for use as a substrate surface immobilized probe that can hybridize to two or more different target nucleic acids that correspond to the same genomic coding sequence, said method comprising:
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(a) selecting at least one consensus sequence for two or more different mRNA transcripts that are transcribed from said same genomic coding sequence, wherein said two or more transcripts may or may not comprise all the known transcripts from said same genomic coding sequence; and
(b) choosing a probe sequence for said at least one consensus sequence to identify said suitable nucleic acid sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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Specification