DNA fingerprint using smith waterman algorithm by grid computing

Orabi, EL-Sayed; Assal, Mohamed A.; Azim, Mustafa Abdel; Kamal, Yasser

doi:10.1109/infos.2014.7036681

Cited by 4 publications

(3 citation statements)

References 5 publications

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“…A DNA sequence can be compared to other DNA sequence through the process of alignment [Orabi et al 2014]. The sequence alignment is a technique to identify regions of similarities among sequences.…”

Section: Bioinformaticsmentioning

confidence: 99%

Contribuições para a ampliação da participação do público feminino nas profissões de tecnologias

Reverdito¹,

Moraes²,

Souza³

et al. 2020

Série Educar- Volume 4 – Tecnologia

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Section: Bioinformaticsmentioning

confidence: 99%

Contribuições para a ampliação da participação do público feminino nas profissões de tecnologias

Reverdito¹,

Moraes²,

Souza³

et al. 2020

Série Educar- Volume 4 – Tecnologia

View full text Add to dashboard Cite

show abstract

“…As an alternative approach, the ability of grid computing of smith waterman algorithm motivated the researchers to analyze the computation time of this algorithm in various implementations. Specifically, the computation time of local DNA sequence alignment is calculated in , adopting the well‐known smith waterman in grid computing. In this implementation, each grid node contains an Intel Corei7‐2600 U CPU @3.45 GHz 4P/4 V cores with 3.701 GHz clock speed and 4.00 GB of RAM.…”

Section: Simulation and Analysismentioning

confidence: 99%

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

Maleki

Koohi

Kavehvash

et al. 2019

Journal of Biophotonics

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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.

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“…Previously Smith-waterman [13] and Needleman-Wunsch algorithm [14] were used in sequence alignment. To increase the efficiency, the Levenshtein distance algorithm [15] is implemented to compute the number of mismatches between two long strings.…”

Section: Introductionmentioning

confidence: 99%

DNA Bar-coding: A Novel Approach for Identifying an Individual Using Extended Levenshtein Distance Algorithm and STR analysis

Likhitha

Ninitha

Kanchana

2016

IJECE

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DNA bar-coding is a technique that uses the short DNA nucleotide sequences from the standard genome of the species in order to find and group the species to which it belongs to. The species are identified by their DNA nucleotide sequences in the same way the items are recognized and billed in the supermarket using barcode scanner to scan the Universal Product Code of the items. Two items may look same to the untrained eye, but in both cases the barcodes are distinct. It was possible to create DNA-barcodes to characterize species by analysing DNA samples from fish, birds, mammals, plants, and invertebrates using Smith-waterman and Needleman-Wunsch algorithm. In this work we are creating human DNA barcode and implementing Extended Levenshtein distance algorithm along with STR analysis that uses less computation time compared to the previously used algorithms to measure the differential distance between the two DNA nucleotide sequences through which an individual can be identified.

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DNA fingerprint using smith waterman algorithm by grid computing

Cited by 4 publications

References 5 publications

Contribuições para a ampliação da participação do público feminino nas profissões de tecnologias

Contribuições para a ampliação da participação do público feminino nas profissões de tecnologias

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

DNA Bar-coding: A Novel Approach for Identifying an Individual Using Extended Levenshtein Distance Algorithm and STR analysis

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