A parallel algorithm for the constrained multiple sequence alignment problem designed for GPUs

DOI10.1142/S0129054112500098MaRDI QIDQ4902884zbMATH OpenOpenAlexFDO

Authors Adam Gudyś, Sebastian Deorowicz

Publication date 18 January 2013

Published in International Journal of Foundations of Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1142/s0129054112500098

zbMATH Keywords

constrained sequence alignmentGPU general processingparallel algorithmsprotein comparison

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

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Cites work

• Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors
• Algorithms on Strings, Trees and Sequences
• An algorithm and applications to sequence alignment with weighted constraints
• Generalized Polykays, an Extension of Simple Polykays and Bipolykays

Cited in

(5)

• Fast vectorized distance matrix computation for multiple sequence alignment on multi-cores
• Parallel Identifying (l,d)-Motifs in Biosequences Using CPU and GPU Computing
• Euro-Par 2004 Parallel Processing
• Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors
• On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures

Describes a project that uses

Uses Software

• CUDA
• Kalign

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