In this work we consider the problem of global DNA sequence alignment. One of the best known and most efficient computational techniques used for this task is the cross-correlation method. We compare efficacy of evaluating periodic DNA sequence misalignment using the standard magnitude-and-phase cross- correlation technique with the lesser known phase-only cross-correlation method. We prove that for a periodic DNA sequence whose length is a prime number the standard approach leads to significant sidelobes in the cross-correlation, the magnitude of which increases with the length of the sequence, while the phase-only approach allows attaining a perfect cross-correlation with zero sidelobes. Numerical experiments on synthesized data are included and robustness of the phase-only method to random DNA insertions and imperfect DNA fragment matches is discussed.
展开▼
