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

DOI10.1142/S0129054112500098zbMATH Open1255.92011OpenAlexW2058772587MaRDI QIDQ4902884FDOQ4902884

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

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zbMATH Keywords

parallel algorithmsconstrained sequence alignmentGPU general processingprotein comparison

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

Cites Work

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

Cited In (4)

• Fast vectorized distance matrix computation for multiple sequence alignment on multi-cores
• 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
• Euro-Par 2004 Parallel Processing

Uses Software

• CUDA
• Kalign

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