SnS-Align

SnS-Align performs hybrid sequence-and-structure pairwise local alignments to detect homologous proteins and demarcate structurally conserved domains across evolutionarily distant organisms.

Key Features:

• Hybrid Alignment Approach: Combines primary amino acid sequences with secondary-structure information to perform pairwise local alignments for improved homology detection.
• Domain Demarcation: Identifies and demarcates structurally conserved domains within superfamilies of paralogous genes.
• Perl Implementation: Implemented as a Perl-based utility for sequence-structure integration and alignment computations.
• Distant-homology Detection: Enhances identification of homologous proteins between evolutionarily distant organisms when sequence similarity alone is insufficient.

Scientific Applications:

• Protein families with complex evolutionary histories: Applied to uncover homologous relationships in families where sequence-based methods are insufficient.
• Gap junction protein superfamily (innexins and pannexins): Used to analyze homologous relationships within innexins and pannexins.
• Myoglobin family: Applied to study evolutionary relationships in the classic myoglobin family.

Methodology:

Performs pairwise local alignments that integrate amino acid sequence and secondary-structure information and identifies structurally conserved domains; implemented in Perl.