#31 · Genomics

QAOA and Grover circuits target phylogeny and genomic motif search

The dominant thread is the encoding of combinatorial genomics problems as quantum sampling or search tasks. The phylogeny study formulates maximum compatibility as weighted independent set enumeration, applies lossless graph reductions to shrink the instance, and uses QAOA-based sampling for the hybrid step. The MotifQu workflow maps k-mer discovery and genome motif scanning onto Grover amplitude amplification, retains genomic coordinate traceability for inspection, and reports that NISQ noise limits amplitude concentration on IBM hardware. The breakpoint-median study is classical rather than quantum. It proves Poisson bounds and overlap limits explaining the corner-seeking and anti-median geometry of breakpoint medians in random signed multichromosomal genomes, and it addresses the same combinatorial genome-rearrangement space. What is new is the explicit reduction of phylogenetic and motif-search problems to variational and amplitude-amplification circuits, with hardware noise identified as limiting the search step.