BioShell

BioShell provides a C++11-based suite of parsers, specialized data structures, and algorithms for processing and analyzing macromolecular sequences, structures, and sequence profiles in structural bioinformatics.

Key Features:

• Parsers: Parsers for macromolecular sequences, structures, and sequence profiles are included to read and process biological data.
• Specialized data structures: Data structures optimized for representing macromolecular entities and associated profiles are provided.
• Algorithms: Algorithms tailored to handle macromolecular sequences, structures, and sequence profiles are implemented.
• C++11 reimplementation (version 2.0): The codebase is rewritten using C++11 to improve modularity and computational efficiency.
• Testing platform: A comprehensive testing platform continuously verifies correctness and integrity and includes over two hundred test programs.

Scientific Applications:

• Structural bioinformatics: Support for analyses focused on macromolecular structure and related sequence-profile data.
• Sequence and structure processing: Processing and analysis of macromolecular sequences, three-dimensional structures, and sequence profiles.
• Bioinformatics application development: Use as a computational foundation for developing bioinformatics applications and web services.

Methodology:

Implementation-level methods explicitly include parsers, specialized data structures, and algorithms for macromolecular data, a C++11-based reimplementation emphasizing modularity and performance, and a continuous testing platform with over two hundred test programs.