Answers.Body: <p>How about trying this?</p>
  <ol>
  <li>Go to <a href="https://www.ncbi.nlm.nih.gov/nucleotide" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/nucleotide</a>. Then type the following command in the search box. It resulted in 23971 items.</li>
  </ol>
  <p><code>(bacterial virus[Organism]) AND (complete genome[ti]) NOT shotgun[ti] NOT plasmid[ti] NOT bacteria[Organism]</code></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-04T14:00:16.330Z
Answers.LastActivityDate: 2022-02-04T14:00:16.330Z
Answers.UserDisplayName: Supertech
Answers.Body: <ol>
  <li><p>Go to the NCBI nuccore database, at <a href="https://www.ncbi.nlm.nih.gov/nuccore" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/nuccore</a>
  Copy and paste the search term:</p>
  <p><code>(bacterial virus[Organism]) AND (3000:110000[sequence length]) NOT bacteria[Organism]</code></p>
  </li>
  </ol>
  <p>You'll get 74583 results.</p>
  <ol start="2">
  <li><p>Click on the link <code>send to</code> and click the checkbox called <code>file</code>.
  It will then download.</p>
  </li>
  <li><p>Check the downloaded file is in <code>fasta format</code> with &quot;&gt;&quot; to start the ID.</p>
  </li>
  <li><p>If fasta format is absent, return to the webpage and where it states <code>summary</code> switch that to <code>fasta text</code></p>
  </li>
  </ol>
  <p>I can't remember if point 4 is needed.</p>
  <p><strong>Notes</strong></p>
  <ul>
  <li>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.</li>
  <li>@acvill informs us that giant phages greater than &gt;200 kb have been annoated. Thus a separate search is likely required targeting this genome size.</li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-02T17:36:37.693Z
Answers.Text: 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](https://www.nature.com/articles/s41586-020-2007-4).
Answers.UserDisplayName: acvill
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Answers.CreationDate: 2022-02-02T18:57:00.727Z
Answers.Text: 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.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-04T14:07:39.877Z
Answers.Text: I did not know you could download all the search results at once as fasta.
Answers.UserDisplayName: Supertech
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-01-28T17:15:42.767Z
Answers.LastActivityDate: 2022-02-02T19:02:20.133Z
Answers.LastEditDate: 2022-02-02T19:02:20.133Z
Answers.UserDisplayName: M__
Body: <p>I am looking to establish the total number of complete phage genomes available on NCBI.</p>
  <p>I am not looking for any specific type, but want to understand the total diversity available.</p>
  <p>How can I perform the search?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-27T14:03:45.760Z
Comments.Text: Could you supply more details? What groups of phages? Any in particular? Every phage? The answer depends on what you are looking for.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-27T16:47:23.503Z
Comments.Text: 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.
Comments.UserDisplayName: pietro_molina
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-27T16:56:05.650Z
Comments.Text: That's easy. Please update your question to clarify this point, because its helps the archives.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-28T10:05:03.827Z
Comments.Text: Done, thank you for guiding me to make the question better suited for the forum.
Comments.UserDisplayName: pietro_molina
Tags: <genome><public-databases><phylogenetics><virus>
Title: How to get the number of complete phage genomes available on ncbi?
ThreadText: # How to get the number of complete phage genomes available on ncbi?
  
  (Asked by: username_0 on 2022-01-27)
  
  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?
  
  **Tags:** genome, public-databases, phylogenetics, virus
  
  > **Comments:**
  > **username_1**: Could you supply more details? What groups of phages? Any in particular? Every phage? The answer depends on what you are looking for.  
  > **username_0**: 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.  
  > **username_1**: That's easy. Please update your question to clarify this point, because its helps the archives.  
  > **username_0**: Done, thank you for guiding me to make the question better suited for the forum.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2022-01-28. Score: 5 | Accepted answer
  
  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.
  * @username_3 informs us that giant phages greater than >200 kb have been annoated. Thus a separate search is likely required targeting this genome size.
  
  > **Comments:**
  > **username_3**: 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](https://www.nature.com/articles/s41586-020-2007-4).  
  > **username_1**: 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.  
  > **username_2**: I did not know you could download all the search results at once as fasta.  
  
  ---
  
  ### Answer by username_2 on 2022-02-04. Score: 2
  
  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]`
  
  
  ---
  
  