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1. Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore Copy and paste the search term:

   (bacterial virus[Organism]) AND (3000:110000[sequence length]) NOT bacteria[Organism]

You'll get 74583 results.

2. Click on the link send to and click the checkbox called file. It will then download.

3. Check the downloaded file is in fasta format with ">" to start the ID.

4. If fasta format is absent, return to the webpage and where it states summary switch that to fasta text

I can't remember if point 4 is needed.

Notes Sequence length, I am guessing that all phages are between 3000 and 105000 in length, this is to screen out partial sequences and to minimise bacteria creeping in to the search. I don't quite understand how a phage can be 105 000bp in length, but you can twiddle these parameters to refine the search.

1. Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore Copy and paste the search term:

   (bacterial virus[Organism]) AND (3000:110000[sequence length]) NOT bacteria[Organism]

You'll get 74583 results.

2. Click on the link send to and click the checkbox called file. It will then download.

3. Check the downloaded file is in fasta format with ">" to start the ID.

4. If fasta format is absent, return to the webpage and where it states summary switch that to fasta text

I can't remember if point 4 is needed.

Notes

• Sequence length, I am guessing that all phages are between 3000 and 105000 in length, this is to screen out partial sequences and to minimise bacteria creeping in to the search. I don't quite understand how a phage can be 105 000bp in length, but you can twiddle these parameters to refine the search.
• @acvill informs us that giant phages greater than >200 kb have been annoated. Thus a separate search is likely required targeting this genome size.

1. Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore Copy and paste the search term:

   (bacterial virus[Organism]) AND (3000:110000[sequence length]) NOT bacteria[Organism]

You'll get 74583 results.

2. Click on the link send to and click the checkbox file It will then download.

3. Check the file is in fasta format with ">" to start the ID.

4. If fasta format is absent, return to the webpage and where it states summary switch that to fasta text

I can't remember if point 4 is needed.

Notes Sequence length, I guess all phages are between 3000 and 105000 in length, this is to screen out partial sequences and to minimise bacteria creeping in to the search. I don't quite understand how a phage can be 105 000bp in length, but you can twiddle these parameters to refine the search.

1. Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore Copy and paste the search term:

   (bacterial virus[Organism]) AND (3000:110000[sequence length]) NOT bacteria[Organism]

You'll get 74583 results.

2. Click on the link send to and click the checkbox called file. It will then download.

3. Check the downloaded file is in fasta format with ">" to start the ID.

4. If fasta format is absent, return to the webpage and where it states summary switch that to fasta text

I can't remember if point 4 is needed.

Notes Sequence length, I am guessing that all phages are between 3000 and 105000 in length, this is to screen out partial sequences and to minimise bacteria creeping in to the search. I don't quite understand how a phage can be 105 000bp in length, but you can twiddle these parameters to refine the search.

1. Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore Copy and paste the search term:

   (bacterial virus[Organism]) AND (3000:110000[sequence length]) NOT bacteria[Organism]

You'll get 74583 results.

2. Click on the link send to and click the check box file It will then download.

3. Check the file is in fasta format with ">" to start the ID.

4. If fasta format is absent return to the webpage and where it states summary switch that to fasta text

I can't remember if point 4 is needed.

Notes Seqence length, I'm guess all phages are between 3000 to 105 000 in length, this is to screen out partial sequences and to minimise bacteria creeping in to the search. I don't quite understand how a phage can be 105 000bp in length, but you can twiddle these parameters to refine the search.

1. Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore Copy and paste the search term:

   (bacterial virus[Organism]) AND (3000:110000[sequence length]) NOT bacteria[Organism]

You'll get 74583 results.

2. Click on the link send to and click the checkbox file It will then download.

3. Check the file is in fasta format with ">" to start the ID.

4. If fasta format is absent, return to the webpage and where it states summary switch that to fasta text

I can't remember if point 4 is needed.

Notes Sequence length, I guess all phages are between 3000 and 105000 in length, this is to screen out partial sequences and to minimise bacteria creeping in to the search. I don't quite understand how a phage can be 105 000bp in length, but you can twiddle these parameters to refine the search.