BIS2Analyzer

BIS2Analyzer identifies co-evolving amino-acid residue pairs in protein alignments to reveal co-adaptation and evolutionary relationships in vertebrate and viral protein families.

Key Features:

• Co-evolution detection: Identifies amino-acid residue pairs that exhibit co-adaptation or correlated evolutionary rates indicative of potential physical interactions and functional relationships.
• BIS2 re-implementation: Implements a fast re-implemented version of the Blocks in Sequences (BIS) algorithm for co-evolution analysis.
• Target sequence sets: Optimized for protein families with small numbers of highly similar homologous sequences, including vertebrate and viral proteins.
• Homology-based analysis: Analyzes homologous sequences and protein alignments to detect co-evolutionary signatures arising from residue co-adaptations or external evolutionary forces.

Scientific Applications:

• Evolutionary biology: Infers evolutionary relationships and compensatory changes between residues within protein families.
• Structural biology: Guides hypotheses about physical residue contacts and structural constraints based on co-evolving positions.
• Functional genomics: Suggests functional linkages between residues that may underlie protein activity or regulation.
• Viral evolution and host–pathogen interactions: Supports analysis of rapid evolutionary changes and compensatory mutations in viral proteins and host-pathogen systems.

Methodology:

Analyzes homologous protein sequences and alignments using the BIS2 re-implementation of the Blocks in Sequences (BIS) algorithm to detect co-evolutionary signatures arising from specific residue co-adaptations or from external forces that similarly affect evolutionary rates.