CHAOS DIALIGN WWW server

CHAOS DIALIGN WWW server aligns large genomic sequences by combining CHAOS local similarity detection with DIALIGN anchored global alignment to produce accurate multiple sequence alignments for comparative genomics.

Key Features:

• Integration of CHAOS and DIALIGN: CHAOS detects chains of local pairwise similarities (anchor points) which DIALIGN uses for global alignment.
• Anchored-alignment strategy: CHAOS identifies strong local pairwise similarities that serve as anchors enabling DIALIGN to align intervening regions more effectively.
• Speed and sensitivity: The use of CHAOS-generated anchors allows DIALIGN to balance computational speed with alignment sensitivity.
• Efficiency for large genomic sequences: Using CHAOS anchors reduces DIALIGN running time by over 95% for BAC-sized and longer genomic sequences while maintaining alignment quality.
• Functional-site detection: Demonstrated capacity to identify exons and small regulatory elements, including alignment of short regulatory sequences around the stem-cell-leukemia (SCL) gene in distant orthologues.

Scientific Applications:

• Cross-species sequence comparison: Produces multiple alignments suitable for identifying conserved regions among orthologues in comparative genomics studies.
• Functional site identification: Enables detection of exons and short regulatory elements in genomic sequences.
• Genome-scale alignment: Applicable to BAC-sized and larger genomic regions for genomic annotation and comparative analysis.

Methodology:

CHAOS rapidly identifies chains of local pairwise similarities across input sequences, and DIALIGN uses these CHAOS-derived anchor points to perform global alignments.