STRAP

STRAP facilitates generation, refinement, and analysis of multiple protein sequence alignments by incorporating structural information such as spatial distances between C(alpha) atoms to improve alignment accuracy and visualization.

Key Features:

• Multiple sequence alignment generation and refinement: Generates, refines, and analyzes multiple protein sequence alignments.
• Structural integration: Integrates structural information into sequence alignments by visualizing spatial distances between C(alpha) atoms.
• Supported input formats: Parses SwissProt, GenBank, EMBL, DSSP, PDB, MSF, and plain ASCII text file formats.
• Scalability: Handles large-scale alignments involving numerous sequences.
• Embedded viewers and modeling programs: Integrates INSIGHT, RASMOL, and WEBMOL for protein structure viewing and modeling.
• Mutation and polymorphism mapping: Maps mutations and polymorphisms onto protein structures.
• Figure generation: Produces high-quality figures suitable for publication.
• Extensible architecture and prototyping: Supports rapid prototyping and testing of complex algorithms, including automatic alignment methods and phylogenetic analyses.

Scientific Applications:

• Structure-guided alignment refinement: Improves alignments in regions of low sequence similarity by incorporating structural distances between C(alpha) atoms.
• Variant interpretation: Maps mutations and polymorphisms onto structures to assess potential structural impacts.
• Protein family and evolutionary analysis: Enables large-scale analysis of protein families and supports phylogenetic analyses.
• Algorithm development and benchmarking: Provides an environment for prototyping and testing automatic alignment methods and phylogenetic algorithms.

Methodology:

Parses SwissProt, GenBank, EMBL, DSSP, PDB, MSF and plain ASCII text; visualizes spatial distances between C(alpha) atoms to incorporate structural information into alignments; integrates INSIGHT, RASMOL and WEBMOL for structure viewing and modeling; maps mutations and polymorphisms onto structures; generates publication-quality figures; and supports prototyping and testing of automatic alignment methods and phylogenetic analyses.