Analysis of DNA sequences by an optical time-integrating correlator

Brousseau, N.; Brousseau, Roland; Salt, J.; Gutz, L.; Tucker, M. D.

doi:10.1364/ao.31.004802

Cited by 4 publications

(4 citation statements)

References 24 publications

(31 reference statements)

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“…Finally, since the phaseonly filter concept have been conceived in the field of optical signal processing, one has to consider a potential optical implementation of the SPOMF sequence aligner. Such an implementation was in fact proposed several years ago [10], and if technologically feasible, might deliver the most efficient solution to the sequence alignment problem.…”

Section: Comparison Of Spomf and Blastmentioning

confidence: 99%

Phase-only filtering for the masses (of DNA Data): a new approach to sequence alignment

Brodzik

2006

IEEE Trans. Signal Process.

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Alignment of DNA segments containing repetitive nucleotide base patterns is an important task in several genomics applications, including DNA sequencing, DNA fingerprinting, pathogen detection, and gene finding. One of the most efficient procedures used for this task is the cross correlation method. The main computations of the procedure are the discrete Fourier transform (DFT) and a pointwise multiplication of two complex Fourier transform sequences. In this paper, the standard magnitude-and-phase cross correlation technique is compared with the lesser known but closely related phase-only cross correlation method. It is shown that for a periodic DNA sequence, the standard approach leads to significant sidelobes in the cross correlation, the magnitude of which increases with sequence length, while the phase-only approach yields a perfect cross correlation with zero sidelobes. For a DNA sequence that contains both irregularly distributed symbols and periodic patterns, the difference in performance is less pronounced, but still significant. Numerical experiments on synthesized and real data demonstrate that the phase-only approach is robust to isolated symbol insertions and deletions and that it is capable of identifying positions of matching segments in the sequence.

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Section: Comparison Of Spomf and Blastmentioning

confidence: 99%

Phase-only filtering for the masses (of DNA Data): a new approach to sequence alignment

Brodzik

2006

IEEE Trans. Signal Process.

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“…It should be noted that since our coding scheme utilizes four bits for representing each character, it stands to reason that the correlation output should be down-sampled, in order to relax ambiguous matches resulted from codes overlap. 27…”

Section: Results and Evaluationmentioning

confidence: 99%

“…So far, various optical DNA alignment approaches 25,27,28,34 have been proposed to perform correlation on two signals or images for detecting exact match among DNA strings. Although there might be some edits in one sequence that mess up exact matching, there still exist a large similarity among DNA strings that must be founded.…”

Section: Problem Definitionmentioning

confidence: 99%

“…So far, various approaches such as optical correlation 23 and Moiré matching techniques 24,25 have been proposed to perform DNA sequence alignment by the means of optical computing process. In correlation based methods, 23,[26][27][28] DNA sequence alignment is performed through an optical correlator to detect regions with high score of similarity (referred to as global alignment).…”

Section: Introductionmentioning

confidence: 99%

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