Anchored DIALIGN

Anchored DIALIGN performs multiple sequence alignment of protein and nucleic acid sequences using the DIALIGN algorithm with user-defined anchor points to constrain and guide homologous segment alignment.

Key Features:

• User-Defined Anchor Points: Allows specification of sequence regions expected to be homologous that act as constraints during alignment.
• Semi-Automatic Alignment: Combines user-specified constraints with automated alignment of remaining regions using the DIALIGN algorithm.
• Biologically Meaningful Alignments: Produces alignments that can reflect biological hypotheses and preserve functionally important protein domains when anchors are provided.
• Integration with TRACKER: The anchored alignment approach has been integrated into the TRACKER software system.

Scientific Applications:

• Genomic Sequences (Hox gene cluster): Applied to genomic regions around the Hox gene cluster to handle complex alignments with user-defined constraints.
• DNA-Binding Proteins: Used for aligning sets of DNA-binding proteins to improve alignment accuracy and relevance via anchor points.

Methodology:

Employs the DIALIGN algorithm with a greedy alignment strategy guided by user-defined anchor constraints, and analysis of anchor effects informs refinement of DIALIGN's objective function.