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

A sequence and biological technology, applied in the field of resequencing microarray design, can solve problems such as increasing computational requirements

CN101535802AInactive Publication Date: 2009-09-16THE UNITED STATES OF AMERICA AS REPRESENTED BY THE SECRETARY OF THE NAVY

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Patent Information

Authority / Receiving Office: CN · China
Current Assignee / Owner: THE UNITED STATES OF AMERICA AS REPRESENTED BY THE SECRETARY OF THE NAVY
Publication Date: 2009-09-16
Estimated Expiration: Not applicable · inactive patent

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Abstract

A computer-implemented method as follows. Providing a list of target sequences associated with one or more organisms in a list of 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 having a predetermined, fixed subsequence length of the corresponding candidate prototype sequence. 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, each set of fragments having every fragment having a predetermined, fixed fragment length of the corresponding target sequence. Calculating the binding free energy of each fragment with a perfect complimentary sequence of the fragment. If any binding free energy is above a predetermined, fixed threshold, the fragment is extended one nucleotide at a time until the binding free energy is below the threshold or the fragment is the same length as the probe, generating a set of extended fragments. Determining which extended fragments are perfect matches to any of the probes. Assembling a base call sequence corresponding to each candidate prototype sequence. The base call sequence has a base call corresponding to the center nucleotide of each probe of the corresponding prototype sequence that is a perfect match to any extended fragment, but for which the other members of the set of probes containing the perfect match probe are not perfect matches to any extended fragment and a non-base call in all other circumstances.

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Description

[0001] This application claims the benefit of US Provisional Patent Application No. 60 / 823,101, filed August 22, 2006, and US Provisional Patent Application No. 60 / 823,510, filed August 25, 2006. This application is a continuation-in-part of U.S. Patent Application No. 11 / 177,646 filed July 22, 2005, U.S. Patent Application No. 11 / 177,647 filed July 2, 2005, and November 7, 2005 U.S. Patent Application No. 11 / 268,373 filed June 6, 2006, U.S. Patent Application No. 11 / 422,431 filed June 6, 2006, and U.S. Patent Application No. 11 / 422,431 filed November 14, 2006 Patent Application No. 11 / 559,513. These applications claim priority to the following provisional patent applications: U.S. Provisional Patent Application No. 60 / 590,931, filed July 2, 2004; U.S. Provisional Patent Application No. 60 / 609,918, filed September 15, 2004; U.S. Provisional Patent Application No. 60 / 626,500 filed Nov. 5, U.S. Provisional Patent Application No. 60 / 631,437 filed Nov. 29, 2004, U.S. Provisional Pa...

Claims

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