Richard's SEA-PHAGES 2020 Page - UNDER CONSTRUCTION

Install DNA Master

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

Follow steps here to Setting DNA Master Preferences

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 - Blast

Save DNA Master file

Blast

Saving your DNA Master file

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?

Run GeneMarkS from phagesdb.org to analyze coding potential

1. Example Genome
2. Run GeneMark (smeg) > save the pdf file
3. For later, analyze coding potential

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 – find similar alignments for later consideration

1. https://phagesdb.org/blast/
2. BLASTing your phage genome sequence against the Actinobacteriophage database

Blast in NCBI – find similar alignments for later consideration

1. https://blast.ncbi.nlm.nih.gov/Blast.cgi
2. BLASTP against the nr database at NCBI

Phamerator – find similar Genes in same “cluster?”

1. https://phamerator.org/
2. Login > Genome Map
3. Phamerator article