One-Block CYRCA

One-Block CYRCA identifies conserved local ungapped protein-region blocks and detects their integration into multiple-block alignments to reveal sequence, structural, and functional relationships using LAMA and CYRCA block-to-block alignment methods.

Key Features:

• Block Identification: Identifies blocks as local ungapped profiles representing the most conserved regions within protein families and domains.
• Block-to-Block Alignment: Employs LAMA (Local Alignment of Multiple Alignments) and CYRCA (Cyclic Redundancy Check Alignment) block-to-block alignment methods to determine whether query blocks form new multiple-block alignments or integrate with existing ones.
• Single-Block Query Expansion: Automates detection of multiple-block alignments originating from single block queries to extend conserved-region relationships.
• Pre-computation via Blocks database: Utilizes pre-computed LAMA block alignments and CYRCA sets from the Blocks database to reduce computation for large-scale analyses.

Scientific Applications:

• Detection of weak sequence relationships: Identifies weak sequence relationships between conserved protein regions, exemplified by relations between flavoprotein subunits in oxidoreductase families and potential active sites.
• Functional and structural similarity analysis: Detects sets of consistently aligned blocks corresponding to regions with similar functions and structures, including similarities between the Rossmann fold ligand-binding region, TIM barrel, and methylase regions.
• Domain-level structure prediction from short regions: Predicts domain structural similarity based on short sequence-region alignments (less than 20 amino acids), including inferred TIM-barrel folds in various protein families.

Methodology:

Uses LAMA and CYRCA block-to-block alignment methods on blocks (local ungapped profiles) and leverages pre-computed LAMA block alignments and CYRCA sets from the Blocks database to automate detection of multiple-block alignments from single-block queries.