A COMPARATIVE STUDY OF CROSS-CORRELATION METHODS FOR ALIGNMENT OF DNA SEQUENCES CONTAINING REPETITIVE PATTERNS (WedPmOR2)

Author(s) : Andrzej Brodzik (MITRE Corporation, United States)

Abstract : 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 method 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 are included and robustness of the phase-only method to random DNA insertions and imperfect DNA fragment matches is discussed.

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