PFAM

Understanding Pfam: The Gateway to Protein Family Analysis

Pfam stands as a fundamental resource in protein research, offering researchers detailed insights into protein families, domains, and evolutionary relationships through sophisticated computational approaches.

Core Components

1. Database Content Primary Features:

• Protein families
• Domain definitions
• Multiple alignments
• Hidden Markov Models
• Functional annotations
• Evolutionary relationships

2. Classification System Organization:

• Pfam-A (curated)
• Clans (related families)
• Domain architectures
• Family relationships
• Sequential features
• Structural mappings

Key Features

1. Search Capabilities Search Options:

• Sequence search
• Domain architecture
• Family browsing
• Keyword search
• Text mining
• Structure mapping

2. Analysis Tools Built-in Tools:

• HMM scanning
• Multiple alignment
• Tree generation
• Domain visualization
• Architecture analysis
• Sequence annotation

Research Applications

1. Protein Analysis Primary Uses:

• Domain identification
• Function prediction
• Evolutionary studies
• Structure prediction
• Annotation transfer
• Family classification

2. Comparative Genomics Applications:

• Domain architecture
• Family distribution
• Evolutionary patterns
• Functional annotation
• Cross-species comparison