ProdomCG_tree

ProdomCG_tree generates phylogenetic trees of protein domain families from completed genomes using domain entries from the ProDom database derived from SWISS-PROT and TrEMBL and integrating Pfam-A annotations.

Key Features:

• Integration with SWISS-PROT and TrEMBL: Uses ProDom entries automatically generated from SWISS-PROT and TrEMBL to represent protein domain families.
• Incorporation of Pfam-A entries: Includes Pfam-A entries to incorporate expert-curated domain models into analyses.
• Stable accession numbers: Assigns stable accession numbers to protein domains for consistent identification and retrieval.
• Consistency indicators: Provides consistency indicators for assessing the reliability of domain assignments within sub-families.
• Domain arrangements: Reports detailed domain arrangements within sub-families for structural and evolutionary inspection.
• Links to Pfam-A: Provides direct links to Pfam-A entries for cross-referencing and validation.

Scientific Applications:

• Phylogenetic analysis: Reconstruct evolutionary relationships among protein domain families using the generated phylogenetic trees.
• Domain architecture analysis: Analyze domain arrangements within completed genomes to study structural and functional evolution of proteins.
• Domain validation and cross-referencing: Validate and cross-reference domain families against Pfam-A to support curated annotation and comparative analyses.

Methodology:

Systematic analysis of protein domains from ProDom (derived from SWISS-PROT and TrEMBL) applied to completed genomes to generate phylogenetic trees, with integration of Pfam-A annotations, assignment of stable accession numbers, and computation of consistency indicators and domain arrangement reports.