Overview
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