<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>

CC BY-SA 4.0
2022-02-04T14:00:16.330Z
2022-02-04T14:00:16.330Z
Supertech
<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>

CC BY-SA 4.0
2022-02-02T17:36:37.693Z
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).
acvill
CC BY-SA 4.0
2022-02-02T18:57:00.727Z
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.
M__
CC BY-SA 4.0
2022-02-04T14:07:39.877Z
I did not know you could download all the search results at once as fasta.
Supertech
CC BY-SA 4.0
2022-01-28T17:15:42.767Z
2022-02-02T19:02:20.133Z
2022-02-02T19:02:20.133Z
M__
<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>

CC BY-SA 4.0
2022-01-27T14:03:45.760Z
Could you supply more details? What groups of phages? Any in particular? Every phage? The answer depends on what you are looking for.
M__
CC BY-SA 4.0
2022-01-27T16:47:23.503Z
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.
pietro_molina
CC BY-SA 4.0
2022-01-27T16:56:05.650Z
That's easy. Please update your question to clarify this point, because its helps the archives.
M__
CC BY-SA 4.0
2022-01-28T10:05:03.827Z
Done, thank you for guiding me to make the question better suited for the forum.
pietro_molina
<genome><public-databases><phylogenetics><virus>
How to get the number of complete phage genomes available on ncbi?
# 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.
* @acvill 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]`


---

