Speeding up DNA sequence alignment by optical correlator

Mozafari, Fereshte; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

doi:10.1016/j.optlastec.2018.06.027

Cited by 8 publications

(12 citation statements)

References 43 publications

(45 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…To increase coding efficiency and reduce size of the input pattern, in [ 14 , 4 ], single value nucleotide coding has been proposed. In these papers, a 4-bit binary coding and integer coding of bio data are proposed, respectively, to minimize size of the input pattern on SLM.…”

Section: Related Workmentioning

confidence: 99%

“…Specifically, recent studies have proposed optical correlators for performing biological sequence alignment [ 4 , 14 , 15 ]. It is worth noting that implementation of an optical correlator is not only helpful in the field of molecular biology, but also can ease data comparison within various signal processing areas, such as speech recognition, computer science [ 16 ], and image recognition (e.g.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

2021

Self Cite

View full text Add to dashboard Cite

In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome, we can improve sensitivity and speed more than 86% and 81%, respectively, compared to BLAST by using coding set generated by GAC method fed to the proposed optical correlator system. Moreover, we present a comprehensive report on the impact of 1D and 2D cross-correlation approaches, as-well-as various coding parameters on the output noise, which motivate the system designers to customize the coding sets within the optical setup.

show abstract

Section: Related Workmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…As concerns the systems that perform optical correlation, one can mention that among their advantages are their very good capabilities of data transfer speed and enhanced capacity for analysis of data [ 4 ]. By using optics instead of numerical solutions, one can benefit from the possibility of using its intrinsic parallelism of processing, from a wide range of specific optical parameters that can be controlled (quantum properties, wavelength, phase, polarization), from noise robustness, increased discrimination ability, shift invariance and less strict requirements of power consumption than in an electronic computer, where electrical processing and cooling require a high amount of energy consumption [ 9 , 16 , 17 , 18 , 19 , 20 ]. As concerns the methods of optical correlation for image recognition, the implementation is easy, both numerically (by two Fourier transforms) and optically (with the use of two lenses) [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Optical Correlators for Cryptosystems and Image Recognition: A Review

Drăgulinescu

2023

Sensors

View full text Add to dashboard Cite

Optical correlators are efficient optical systems that have gained a wide range of applications both in image recognition and encryption, due to their special properties that benefit from the optoelectronic setup instead of an all-electronic one. This paper presents, to the best of our knowledge, the most extensive review of optical correlators to date. The main types are overviewed, together with their most frequent applications in the newest contributions, ranging from security uses in cryptosystems, to medical and space applications, femtosecond pulse detection and various other image recognition proposals. The paper also includes a comparison between various optical correlators developed recently, highlighting their advantages and weaknesses, to gain a better perspective towards finding the best solutions in any specific domain where these devices might prove highly efficient and useful.

show abstract

“…To overcome the above limitations, which are inherent to electrical computers, optical computation has been proposed to perform global alignment in real time by various studies . However, despite their fast performance, these methods fail to detect mutations/indels in short sequences, which is required for local alignment.…”

Section: Introductionmentioning

confidence: 99%

OptCAM: An ultra‐fast all‐optical architecture for DNA variant discovery

Maleki

Koohi

Kavehvash

et al. 2019

Journal of Biophotonics

Self Cite

View full text Add to dashboard Cite

Nowadays, the accelerated expansion of genetic data challenges speed of current DNA sequence alignment algorithms due to their electrical implementations. Essential needs of an efficient and accurate method for DNA variant discovery demand new approaches for parallel processing in real time. Fortunately, photonics, as an emerging technology in data computing, proposes optical correlation as a fast similarity measurement algorithm; while complexity of existing local alignment algorithms severely limits their applicability. Hence, in this paper, employing optical correlation for global alignment, we present an optical processing approach for local DNA sequence alignment to benefit both high‐speed processing and operational parallelism, inherently exist in optics. The proposed method, named as OptCAM, utilizes amplitude and wavelength of the optical signals, to accurately locate mutations through three main procedures. Furthermore, an all‐optical implementation of the OptCAM method is proposed consisting of three units, corresponding to the three OptCAM procedures. Performing considerably fast processes by passing optical signals through high‐throughput photonic devices, OptCAM avoids various limitations of electrical implementations. Accuracy and efficiency of the OptCAM method and its optical implementation are validated through numerical simulation by a gold standard simulation benchmark. The results indicate the proposed method is significantly faster than its electrical counterparts, in both single node and grid computation.

show abstract

Speeding up DNA sequence alignment by optical correlator

Cited by 8 publications

References 43 publications

Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

Optical Correlators for Cryptosystems and Image Recognition: A Review

OptCAM: An ultra‐fast all‐optical architecture for DNA variant discovery

Contact Info

Product

Resources

About