SCANPS

SCANPS performs iterative protein-sequence database searches using full dynamic programming and on-the-fly significance estimation to improve sensitivity and selectivity for protein domain identification.

Key Features:

• Iterative Profile Searching: Employs complete dynamic programming for every iteration of profile-based protein sequence searching.
• On-the-Fly Significance Estimation: Estimates statistical significance of search results during each search cycle.
• Sensitivity and Selectivity vs PSI-BLAST: Demonstrates higher sensitivity and selectivity than PSI-BLAST in domain-searching benchmarks.
• Computational Acceleration: Implements on-chip parallelism via MMX and SSE2 instructions on Intel processors and MPI-based parallelism.
• Database Compatibility: Supports searches against SCOP and a wide range of protein sequence databases.
• SCOP Tree-Based Representation: Presents SCOP search results in a tree-based representation that mirrors the SCOP hierarchy to contextualize hits.

Scientific Applications:

• Protein Domain Identification: Enhances detection of protein domains through iterative, profile-based searches.
• Homology Detection: Identifies homologous sequences with improved sensitivity and selectivity compared to PSI-BLAST.
• Structural Classification Mapping: Maps sequence hits to SCOP classifications and their hierarchical relationships.
• Protein Function and Evolution Inference: Supports inference of protein function and evolutionary relationships via improved homolog detection.
• Benchmarking Domain-Search Methods: Serves in evaluations of sensitivity and selectivity in domain-searching benchmarks.

Methodology:

Iterative profile searching using complete dynamic programming in each cycle with on-the-fly significance estimation; computational acceleration via MMX and SSE2 on Intel processors and MPI parallelism.