A parallel strategy for biological sequence alignment in restricted memory space

DOI10.1016/J.JPDC.2007.08.007MaRDI QIDQ436758zbMATH OpenOpenAlexFDO

Authors Rodolfo Bezerra Batista, Azzedine Boukerche, Alba Cristina Magalhaes Alves De Melo

Publication date 26 July 2012

Published in Journal of Parallel and Distributed Computing (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jpdc.2007.08.007

zbMATH Keywords

DNA sequencinghigh performance computingbiological inspired technique

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Parallel algorithms in computer science (68W10) Algorithms on strings (68W32)

Recommendations

• Parallel strategies for the local biological sequence alignment in a cluster of workstations
• Exact parallel alignment of megabase genomic sequences with tunable work distribution
• Experimental and Efficient Algorithms
• Parallel divide and conquer bio-sequence comparison based on Smith-Waterman algorithm
• FastLSA: A fast, linear-space, parallel and sequential algorithm for sequence alignment

Cites work

• scientific article; zbMATH DE number 808499 (Why is no real title available?)
• A linear space algorithm for computing maximal common subsequences
• Algorithms on Strings, Trees and Sequences
• Experimental and Efficient Algorithms
• FastLSA: A fast, linear-space, parallel and sequential algorithm for sequence alignment
• Optimal sequence alignment using affine gap costs
• Parallel biological sequence comparison using prefix computations.
• Parallel divide and conquer bio-sequence comparison based on Smith-Waterman algorithm

Cited in

(8)

• Parallel divide and conquer bio-sequence comparison based on Smith-Waterman algorithm
• Fast vectorized distance matrix computation for multiple sequence alignment on multi-cores
• Accelerating computation of DNA sequence alignment in distributed environment
• Exact parallel alignment of megabase genomic sequences with tunable work distribution
• FastLSA: A fast, linear-space, parallel and sequential algorithm for sequence alignment
• Experimental and Efficient Algorithms
• Parallel strategies for the local biological sequence alignment in a cluster of workstations
• scientific article; zbMATH DE number 1955849 (Why is no real title available?)

Describes a project that uses

Uses Software

• FastLSA

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