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Design and selection of genetic targets for sequence resolved organism detection and identification

Patent image
NRL

A computer-implemented method as follows. Providing a list of target sequences associated with one or more organisms. Providing a list of candidate prototype sequences suspected of hybridizing to one or more of the target sequences. Generating a collection of probes corresponding to each candidate prototype sequence, each collection of probes having a set of probes for every subsequence. The sets consist of the corresponding subsequence and every variation of the corresponding subsequence formed by varying a center nucleotide of the corresponding subsequence. Generating a set of fragments corresponding to each target sequence. Calculating the binding free energy of each fragment with a perfect complimentary sequence of the fragment. Determining which extended fragments are perfect matches to any of the probes. Assembling a base call sequence corresponding to each candidate prototype sequence.

Inventors: 
Malanoski, Anthony P.; Wang, Zheng; Lin, Baochuan; Stenger, David A.; Schnur, Joel M.
Patent Number: 
Technical domain: 
Materials and Coatings
FIle Date: 
2007-08-22
Grant Date: 
2010-02-23
Grant time: 
916 days
Grant time percentile rank: 
16
Claim count percentile rank: 
4
Citations percentile rank: 
1
'Cited by' percentile rank: 
1
Assignee: 
US NAVY