Efficient Parallel Design for Edit distance algorithm in DNA Sequence Alignment
نویسندگان
چکیده
The focus of Bioinformatics research is usually on two aspects—genomics and proteomics, specifically, it’s starting from nucleic acid and protein sequences, analyzing the structural and functional biological information expressed in the sequences. Biological sequence alignment is one of the common problems, the NeedlemanWunsch algorithm based on dynamic programming is the most basic algorithm, and Edit Distance(Levenshtein Distance) algorithm is also widely used in DNA sequence alignment. Nowadays, there are large amount of improvements on the Needleman-Wunsch algorithm, while few on Edit Distance algorithm, so this paper focuses on revealing the effects of parallel design on optimizing the Edit Distance algorithm, and it also compares the two algorithms’ different significances in DNA sequence alignment objectively.
منابع مشابه
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping
MOTIVATION Calculating the edit-distance (i.e. minimum number of insertions, deletions and substitutions) between short DNA sequences is the primary task performed by seed-and-extend based mappers, which compare billions of sequences. In practice, only sequence pairs with a small edit-distance provide useful scientific data. However, the majority of sequence pairs analyzed by seed-and-extend ba...
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Motivation: Calculating the edit-distance (i.e. minimum number of insertions, deletions and substitutions) between short DNA sequences is the primary task performed by seed-and-extend based mappers, which compare billions of sequences. In practice, only sequence pairs with a small editdistance provide useful scientific data. However, the majority of sequence pairs analyzed by seedand-extend bas...
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