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US 7,396,646 B2Granted
Alien sequences
AssigneesModular Genetics, Inc., Trustees of Boston University
InventorsSean Quinlan, Temple Smith, Prashanth Vishwanath
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Abstract
The present invention provides sequences and reagents for preparing microarrays with internal controls. Specifically, the present invention defines and provides sequences that are not present in the hybridizing mRNA or cDNA, and therefore can be used both as hybridization controls and for inter-spot normalization.
Claims19
A method of generating an alien sequence comprising steps of:
- A) providing a naturally-occurring sequence;
- B) determining one or more natural sequence statistics of the naturally-occurring sequence;
- C) applying a Hidden Markov Model algorithm to the one or more natural sequence statistics of the naturally-occurring sequence to generate an alien sequence, wherein the sequence statistic is selected from the group consisting of:
- codon occurrence, codon boundary di-nucleotide frequencies, and combinations thereof;
- D) generating and displaying the alien sequence, with the proviso that, at an adjustable frequency, at least one of the natural sequence statistics of the naturally-occurring sequence is switched to a sequence statistic that is inversely proportional to the natural sequence statistic,
- such that the alien sequence comprises intermittent highly improbable sequence patterns or subsequences throughout its length.
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Dependencies are inferred from the claim text.