Malakite

Malakite identifies and validates reliable aligned blocks within protein multiple sequence alignments to extract regions of genuine evolutionary kinship and support structural and evolutionary analyses.

Key Features:

• Detection of reliable aligned blocks: Identifies and isolates blocks within protein multiple sequence alignments that contain sequences related through evolutionary kinship.
• Alignment analysis functions: Provides analytical functions to scrutinize and refine alignments by focusing on segments with substantiated homology.
• Verification against structural data: Compares detected aligned blocks to structural data to confirm that identified regions reflect true biological relationships.

Scientific Applications:

• Structural Biology: Supplies reliable aligned regions for inferring structural and functional relationships between proteins.
• Evolutionary Studies: Supports phylogenetic and evolutionary analyses by ensuring comparisons are restricted to homologous regions.
• Protein Engineering and Design: Enables precise identification of conserved regions critical for rational protein design and engineering.

Methodology:

Detection and isolation of aligned blocks from multiple sequence alignments and validation by comparison against structural data (MAlAKiTE — Multiple Alignment Automatic Kinship Tiling Engine).