ALIGN

ALIGN implements pairwise sequence alignment techniques as a C++ class library to support protein sequence comparison and protein structure prediction.

Key Features:

• C++ class library: Implemented as a C++ object-oriented class library for pairwise sequence alignment.
• Versatile alignment techniques: Supports sequence-to-sequence and profile-to-profile pairwise alignments.
• Secondary structure incorporation: Integrates secondary structure information into the alignment process.
• Suboptimal alignments: Generates suboptimal alignments to estimate regions of alignment confidence.
• Object-oriented design: Provides modularity and extensibility for implementing, testing, and extending alignment functionalities.

Scientific Applications:

• Protein structure prediction: Produces alignments used to inform prediction and comparative modeling of protein structures.
• Modeling studies (human Cytochrome P450): Has been applied in modeling studies including human Cytochrome P450.

Methodology:

Implements pairwise sequence alignment techniques in a C++ object-oriented library, supporting sequence-to-sequence and profile-to-profile alignments, inclusion of secondary structure information, and generation of suboptimal alignments.