Patent ID: 7668664

Claim:
A computer-implemented method comprising: 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 comprising a set of probes for every subsequence having a predetermined, fixed subsequence length of the corresponding candidate prototype sequence, the set consisting 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 comprising every fragment having a predetermined, fixed fragment length of the corresponding target sequence; calculating the binding free energy of each fragment with a perfect complementary sequence of the fragment, and 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 probes corresponding to the corresponding target sequence, generating a set of extended fragments; and determining which extended fragments are perfect matches to any of the probes; and assembling a base call sequence corresponding to each candidate prototype sequence comprising: 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; wherein the method is at least partly performed using a suitably programmed computer.