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I am looking to establish the total number of complete phage genomes available on NCBI.

I am not looking for any specific type, but want to understand the total diversity available.

How can I perform the search?

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  • $\begingroup$ Could you supply more details? What groups of phages? Any in particular? Every phage? The answer depends on what you are looking for. $\endgroup$
    – M__
    Jan 27, 2022 at 14:03
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    $\begingroup$ The idea is to get the total number of complete phage genomes available on ncbi. So yes, I am not looking for any particular kind, just want to know how many are there. $\endgroup$ Jan 27, 2022 at 16:47
  • $\begingroup$ That's easy. Please update your question to clarify this point, because its helps the archives. $\endgroup$
    – M__
    Jan 27, 2022 at 16:56
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    $\begingroup$ Done, thank you for guiding me to make the question better suited for the forum. $\endgroup$ Jan 28, 2022 at 10:05

2 Answers 2

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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.

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

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

  3. 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.
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    $\begingroup$ Anecdotally, (3000:110000[sequence length]) should capture the vast majority of phage genomes, though a growing number of huge phages (>200 kb) are being annotated. $\endgroup$
    – acvill
    Feb 2, 2022 at 17:36
  • $\begingroup$ Thank you, that is good expert opinion. I will update the post. I am mystified how a virus can be this size in comparison to their bacterial host genome, but phages are not my thing. $\endgroup$
    – M__
    Feb 2, 2022 at 18:57
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    $\begingroup$ I did not know you could download all the search results at once as fasta. $\endgroup$
    – Supertech
    Feb 4, 2022 at 14:07
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How about trying this?

  1. Go to https://www.ncbi.nlm.nih.gov/nucleotide. Then type the following command in the search box. It resulted in 23971 items.

(bacterial virus[Organism]) AND (complete genome[ti]) NOT shotgun[ti] NOT plasmid[ti] NOT bacteria[Organism]

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