This website contains a collection of notes to support the teaching of SEA-PHAGES related courses. Notes include using bioinformatics software to auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics.

Step 1. How it all began

Objective Description Video
How it all begin 2019 Phage Genomics Workshop  
The software = DNA Master

Install DNA Master

- direct installation link, download exe file, and install
- update DNA Master in software:
- "Help > Update DNA Master"

DNA Master - User Preferences

Follow steps here to Setting DNA Master Preferences



Step 2. Auto-annotating a genome

Objective Description Video
The Bioinformatics Guide The Bioinformatics Guide Link  
Download the genome FASTA file

If you want to download an example file for testing/training, you can download BoDEinwohner17 genome for testing.

This is article "Retrieving your finished phage genome sequence".

DNA Master - Auto-Annotation Auto-Annotation: Adding gene predictions to the draft annotation of your genome  

DNA Master - Blast

Save DNA Master file


Saving your DNA Master file

DNA Master – Gene prediction
  1. File > Open > Archived DNA Master File
  2. DNA > Frames
  3. Evaluating protein-coding gene predictions
    • Is it a gene?
    • Where does it start?
    • What’s its function?


step 3. Analyze gene sequence - tools

Objective Description Video
GeneMarkS - coding potential

Run GeneMarkS from to analyze coding potential

  1. Example Genome
  2. Run GeneMark (smeg) > save the pdf file
  3. For later, analyze coding potential
Starterator – start position
  1. Example Genome
  2. Scroll down > Gene List > Click to View (select gene no.) > (next page) Starterator – Pham xxxx report
  3. For later, analyze coding potential
Blast in PhageDB

Blast in PhageDB – find similar alignments for later consideration

  2. BLASTing your phage genome sequence against the Actinobacteriophage database
Blast in NCBI

Blast in NCBI – find similar alignments for later consideration

  2. BLASTP against the nr database at NCBI

Phamerator – find similar Genes in same “cluster?”

  2. Login > Genome Map
  3. Phamerator article 


step 4. COMING SOON...

Objective Description Video