PECAAN
Phage Evidence Collection And Annotation Network

Training Materials

Training Content

  1. Overview of Genome Basics
  2. How to find where genes are located on the genome.
    1. Finding closest relatives
    2. Compare your genome to those of closest relatives
    3. How are the locations of genes predicted
    4. How do you add and delete genes
  3. How do you find the correct start site for a protein coding gene
    1. Gaps
    2. Ribosomal binding site metrics
    3. Coding Capacity
    4. ORF (Open Reading Frame)
    5. Weighing all of the Evidence
  4. How do you find the correct start and stop site for a tRNA or a tmRNA gene
    1. tRNA Gene
    2. tmRNA Gene
  5. How do you annotate translational frameshifts
    1. Tail assembly chaperone protein genes
  6. How do you find the function of a protein coding gene?
    1. PhagesDB
    2. HHPred
    3. NCBI BLAST
    4. Conserved Domain Database
    5. Transmembrane predictions
  7. How do you annotate or quality check the function & synteny of a protein coding gene
    1. Function
    2. Synteny
    3. Notes, final review, and quality checking

PECAAN Video Tutorials

Overview and Genome Basics

Introduction to phage genomes and basic annotation concepts.

Finding closest relatives

Learn how to identify evolutionary relatives of your phage.

Compare genome to closest relatives

Comparative analysis techniques for genome annotation.

How the locations of genes are predicted

Understanding gene prediction algorithms and tools.

How to add and delete genes

Practical guide to modifying gene annotations in PECAAN.

SEA PHAGES annotation guide

Comprehensive guide following SEA PHAGES standards.

Starterator, PhagesDB & NCBI BLAST

Using external tools for start site determination.

Gaps & Ribosomal Binding Sites

Analyzing intergenic regions and RBS sequences.

GM coding capacity, LORF & start sites

Advanced techniques for start site selection.

tRNA and tmRNA

Annotating transfer RNA and transfer-messenger RNA genes.

Assigning a function

Methods for determining protein function and annotation.