Genomic Mapping & Sequence Assays

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Abstractions about DNA replication, repeated sequences, genomic hybridization, radiation mapping, target prediction, and nuclease-based variant detection.

6 abstractions in this family — domain-specific abstractions that sit near one another in structural-signature space (k-means over structural-signature embeddings). Each is shown with its short description.

• Comparative Genomic Hybridization — Infer relative genomic copy-number gains and losses by competitively hybridizing differently labeled test and reference DNA and mapping their normalized signal ratio by locus.
• Direct Repeat — Two or more copies of a nucleotide motif occurring in the same 5′→3′ orientation within one DNA molecule, either adjacent or separated by intervening sequence.
• DNA Replication — Initiation-authorized replisomes separate parental DNA strands and use each as a complementary template for semiconservative synthesis of inheritable daughter DNA.
• Radiation Hybrid Mapping — Infer chromosomal marker order and distance from radiation-induced breakage and co-retention across a panel of hybrid cell lines, without requiring meiotic recombination.
• RNA22 Target-Prediction Algorithm — Predict microRNA binding sites by first discovering recurring sequence patterns in mature microRNAs, scanning candidate transcripts for pattern hits, and then evaluating plausible miRNA–target heteroduplexes without requiring cross-species conservation.
• Surveyor Nuclease Assay — A targeted mismatch-cleavage assay that PCR-amplifies a locus, denatures and reanneals sequence variants into heteroduplexes, uses Surveyor nuclease to cut beside mismatches, and reads fragment sizes and intensities as evidence of variants and approximate editing frequency.