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