An efficient solution for aligning huge DNA sequences

Hosny, Ahmad M.; Shedeed, Howida A.; Hussein, Ashraf S.; Tolba, Mohamed F.

doi:10.1109/icces.2011.6141059

Cited by 4 publications

(2 citation statements)

References 26 publications

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“…In [2] is developed a parallel solution to achieve the optimum alignment with relatively good performance. The shared memory parallel architecture is the focus of this work therefore; it have considered offthe-shelf systems like multi-core CPUs as well as advanced shared memory platforms.…”

Section: Related Workmentioning

confidence: 99%

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Enhanced Dynamic Algorithm of Genome Sequence Alignments

Keshk¹

2014

IJITCS

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Abstract-The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between sequences. This paper introduces an enhancement of dynamic algorithm of genome sequence alignment, which called EDAGSA. It is filling the three main diagonals without filling the entire matrix by the unused data. It gets the optimal solution with decreasing the execution time and therefore the performance is increased. To illustrate the effectiveness of optimizing the performance of the proposed algorithm, it is compared with the traditional methods such as Needleman-Wunsch, Smith-Waterman and longest common subsequence algorithms. Also, database is implemented for using the algorithm in multi-sequence alignments for searching the optimal sequence that matches the given sequence.

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Section: Related Workmentioning

confidence: 99%

“…Aligning two long DNA sequences requires a long time on a single processor and a very large memory capacity [2]. Aligned sequences of nucleotides or amino acids residues are typically represented as rows within a matrix.…”

Section: Introductionmentioning

confidence: 99%