Clustal 2 (Clustal W, Clustal X)

Clustal 2 (Clustal W, Clustal X) performs multiple sequence alignment of nucleotide and protein sequences to support comparative genomics, evolutionary analysis, and protein structure and function inference.

Key Features:

• Improved sensitivity for divergent sequences: Uses individual sequence weighting in partial alignments, dynamic adjustment of amino acid substitution matrices according to sequence divergence at different alignment stages, and residue-specific plus locally reduced gap penalties in hydrophilic regions to favor gap placement in putative loop areas.
• Progressive multiple sequence alignment: Implements a progressive alignment strategy for constructing MSAs from pairwise relationships and profiles.
• Profile alignment capability: Supports alignment of multiple sequences and sequence profiles for combined or iterative alignment tasks.
• Alignment quality analysis: Provides analysis to identify low-scoring segments or exceptional residues to guide iterative refinement and detect input-sequence errors.

Scientific Applications:

• Conserved motif identification: Aligns nucleotide and protein sequences to detect conserved motifs and sequence signatures.
• Evolutionary analysis: Facilitates inference of evolutionary relationships among homologous sequences, including distant homologs.
• Functional domain and structure inference: Supports identification of functional domains and contributes to protein structure and function prediction.
• Study of divergent sequences: Enables analysis of distant homologs and complex evolutionary scenarios by improving alignment sensitivity for highly divergent sequences.

Methodology:

Employs a progressive alignment strategy enhanced by sequence weighting in partial alignments, dynamic/adaptive amino acid substitution matrices adjusted by sequence divergence at different stages, and residue-specific plus locally reduced gap-penalty schemes in hydrophilic regions.