DIALIGN

DIALIGN performs multiple sequence alignment by assembling global alignments from gap-free local pairwise alignments to detect local homologies in sequences with low overall similarity.

Key Features:

• Local homology detection: Identifies locally homologous segments within sequences that exhibit low overall similarity.
• Gap-free local pairwise alignment assembly: Builds global alignments from gap-free local pairwise alignments to align only homologous segments.
• Automated and externally constrained modes: Provides versions that operate automatically and versions that allow incorporation of external information or constraints.
• PFAM integration (DIALIGN-PFAM): Leverages PFAM database hits to guide and enhance protein alignments using domain annotations.
• Reduction of non-homologous noise: Focuses alignment on relevant segments to preserve biologically meaningful regions while minimizing alignment of non-homologous sequence.

Scientific Applications:

• Comparative genomics: Detects conserved local regions across large genomic sequences for cross-species comparisons.
• Evolutionary analysis / Phylogenetics: Identifies local homologous segments useful for inferring evolutionary relationships.
• Large-sequence alignment: Suited for aligning large sequences that share only localized similarity.
• Gene family, motif, and conserved-region studies: Facilitates analysis of gene families, structural motifs, and conserved regions across diverse species.

Methodology:

Constructs global alignments by assembling gap-free local pairwise alignments; DIALIGN-PFAM incorporates PFAM hits to guide protein alignments.