DESIGN AND SELECTION OF GENETIC TARGETS FOR SEQUENCE RESOLVED ORGANISM DETECTION AND IDENTIFICATION

摘要

A computer-implemented method as follows. Providing a list of target sequ ences associated with one or more organisms in a list of organisms. Providin g a list of candidate prototype sequences suspected of hybridizing to one or more of the target sequences. Generating a collection of probes correspondi ng to each candidate prototype sequence, each collection of probes having a set of probes for every subsequence having a predetermined, fixed subsequenc e length of the corresponding candidate prototype sequence. The sets consist of the corresponding subsequence and every variation of the corresponding s ubsequence formed by varying a center nucleotide of the corresponding subseq uence. Generating a set of fragments corresponding to each target sequence, each set of fragments having every fragment having a predetermined, fixed fr agment length of the corresponding target sequence. Calculating the binding free energy of each fragment with a perfect complimentary sequence of the fr agment. If any binding free energy is above a predetermined, fixed threshold , the fragment is extended one nucleotide at a time until the binding free e nergy is below the threshold or the fragment is the same length as the probe , generating a set of extended fragments. Determining which extended fragmen ts 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 fra gment, but for which the other members of the set of probes containing the p erfect match probe are not perfect matches to any extended fragment and a no n-base call in all other circumstances.