  The Quantum Pairwise Sequence Alignment (QPSA) algorithm offers exponential
speedups in data alignment tasks. However, it relies on an open problem of
efficiently encoding the classical data being aligned into quantum
superposition. Previous works suggest the use of specialized nonlinear Kerr
media to implement a black-box oracle that achieves the superposition. We
provide an alternative, explicit construction of this oracle called the Quantum
Dot Plot (QDP), which is compatible with universal gate machines. We evaluate
QDP's operational complexity via analysis of the quantum machine instructions
generated by the Q# and Qiskit software frameworks for various sample circuits.
Our analysis confirms that the data encoding scheme is exponentially difficult,
precluding QDP's (and thus, QPSA's) employment on general-purpose quantum
computers. Nevertheless, we find utility in estimating the circuit depth and
run time of both QDP and QPSA for IBM's superconducting architecture and AQT's
trapped ion architecture for direct comparison and overall practicality
purposes.
