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QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.

Adam Gudyś1, Sebastian Deorowicz1

  • 1Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.

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Summary
This summary is machine-generated.

QuickProbs accelerates multiple sequence alignment (MSA) by redesigning computationally intensive stages for graphics processors (GPUs). This variant of MSAProbs offers significant speed-ups while maintaining or improving alignment accuracy.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is fundamental for various biological analyses.
  • MSAProbs is a highly accurate MSA algorithm but computationally intensive.

Purpose of the Study:

  • To develop a faster variant of MSAProbs suitable for graphics processors (GPUs).
  • To enhance the computational efficiency of MSA while preserving accuracy.

Main Methods:

  • Redesigned two time-consuming stages of MSAProbs (posterior matrices calculation, consistency transformation) for GPU execution using OpenCL.
  • Evaluated QuickProbs on standard benchmarks (BAliBASE, PREFAB, OXBench-X) and Pfam protein families.

Main Results:

  • QuickProbs achieved 5.7 to 9.7 times speed-up over CPU-parallel MSAProbs on a quad-core PC with a high-end GPU.
  • Overall speed-up of 6.7 was observed on Pfam protein families.
  • QuickProbs demonstrated higher accuracy than MAFFT, MUSCLE, and ClustalW at comparable speeds.
  • A tuned variant of QuickProbs showed improved accuracy on distantly related sequences.

Conclusions:

  • QuickProbs offers a significant performance improvement for MSA through GPU acceleration.
  • The OpenCL implementation ensures broad compatibility across different GPU vendors.
  • QuickProbs provides a powerful and accurate tool for large-scale biological sequence analysis.