PECAAN Video Tutorials

Overview and Genome Basics

Finding closest relatives

Compare genome to closest relatives

How the locations of genes are predicted

How to add and delete genes                         

SEA PHAGES annotation guide

Starterator, PhagesDB & NCBI BLAST

Gaps & Ribosomal Binding Sites

GM coding capacity, LORF & start sites

tRNA and tmRNA

Assigning a function

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