Abstract: Techniques for identifying regions in nucleic acid sequences for which to design highly discriminatory primers are provided. In some embodiments, a corpus of nucleic acid sequences may be divided into a first set and a second set, and a respective index may be built containing data structures representing a plurality of k-mers of each nucleic acid sequence. By comparing the data structures of the first index to one another, a system may iteratively determine whether each k-mer over a given region in one of the nucleic acid sequences in the first set are also found in every other sequence in the first set. By comparing against the data structures in the second index, a system may then iteratively determine whether all k-mers in the region can be found in the same order of in any of the nucleic acid sequences in the second set.

Abstract: Techniques for identifying regions in nucleic acid sequences for which to design highly discriminatory primers are provided. In some embodiments, a corpus of nucleic acid sequences may be divided into a first set and a second set, and a respective index may be built containing data structures representing a plurality of k-mers of each nucleic acid sequence. By comparing the data structures of the first index to one another, a system may iteratively determine whether each k-mer over a given region in one of the nucleic acid sequences in the first set are also found in every other sequence in the first set. By comparing against the data structures in the second index, a system may then iteratively determine whether all k-mers in the region can be found in the same order of in any of the nucleic acid sequences in the second set.

Abstract: Techniques for identifying regions in nucleic acid sequences for which to design highly discriminatory primers are provided. In some embodiments, a corpus of nucleic acid sequences may be divided into a first set and a second set, and a respective index may be built containing data structures representing a plurality of k-mers of each nucleic acid sequence. By comparing the data structures of the first index to one another, a system may iteratively determine whether each k-mer over a given region in one of the nucleic acid sequences in the first set are also found in every other sequence in the first set. By comparing against the data structures in the second index, a system may then iteratively determine whether all k-mers in the region can be found in the same order of in any of the nucleic acid sequences in the second set.