PECAAN Overview

What is Phage Genome Annotation?

Phage genome annotation is the process of identifying and describing the functional elements within a bacteriophage (phage) genome. This includes:

• Gene identification: Locating protein-coding genes, tRNAs, and other functional elements
• Functional annotation: Determining what each gene does
• Quality assessment: Ensuring annotations are accurate and well-supported

The Annotation Process

1. Genome Preparation

• Quality assessment of the genome sequence
• Identification of closest relatives
• Initial gene calling and prediction

2. Evidence Collection

• Comparative genomics analysis
• Database searches (BLAST, HHpred, etc.)
• Structural predictions
• Synteny analysis

3. Annotation Refinement

• Start site determination
• Functional assignment
• Quality checking
• Final review and validation

Tools and Resources

PECAAN training covers the use of various bioinformatics tools including:

• PhagesDB: Phage genome database and comparison tools
• NCBI BLAST: Sequence similarity searches
• HHpred: Structure and function prediction
• Starterator: Start site analysis tool

Best Practices

Our training emphasizes:

• Using multiple lines of evidence
• Conservative functional annotations
• Proper documentation and note-taking
• Collaboration and peer review