QuickProbs

QuickProbs performs multiple sequence alignment by implementing GPU-optimized versions of the MSAProbs algorithm to accelerate alignment while preserving or improving accuracy for applications such as secondary structure prediction, domain searching, and phylogenetic analysis.

Key Features:

• GPU Optimization: Uses OpenCL to execute alignment computations on graphics processing units, enabling compatibility across GPU vendors.
• Targeted Redesign: Redesigns the calculation of posterior matrices and the consistency transformation from MSAProbs for execution on GPUs.
• Performance Gains: Demonstrates 5.7–9.7× speed-up over CPU-parallel MSAProbs on BAliBASE, PREFAB, and OXBench-X benchmarks on a quad-core PC with a high-end graphics card, and an overall 6.7× speed-up on Pfam protein families.
• Accuracy: Maintains or surpasses the accuracy of MSAProbs and is reported to be more accurate than MAFFT, MUSCLE, and ClustalW at comparable speeds.
• Enhanced Variant: Provides a tuned variant that improves accuracy for sets of distantly related sequences without exceeding the computational time of MSAProbs.

Scientific Applications:

• Secondary Structure Prediction: Supplies accurate multiple sequence alignments to support protein secondary structure prediction.
• Domain Searching: Identifies conserved regions across sequences to facilitate domain searches.
• Phylogenetic Analysis: Produces alignments suitable for constructing phylogenetic trees and studying evolutionary relationships in large datasets.

Methodology:

Builds upon the MSAProbs algorithm by executing the posterior matrix calculation and consistency transformation on GPUs via OpenCL.