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__ ♦Commented Jan 27, 2022 at 14:03
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1$\begingroup$ 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. $\endgroup$– pietro_molinaCommented Jan 27, 2022 at 16:47
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$\begingroup$ That's easy. Please update your question to clarify this point, because its helps the archives. $\endgroup$– M__ ♦Commented Jan 27, 2022 at 16:56
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1$\begingroup$ Done, thank you for guiding me to make the question better suited for the forum. $\endgroup$– pietro_molinaCommented Jan 28, 2022 at 10:05
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2 Answers
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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.
Click on the link
send toand click the checkbox calledfile. It will then download.Check the downloaded file is in
fasta formatwith ">" to start the ID.If fasta format is absent, return to the webpage and where it states
summaryswitch that tofasta 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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2$\begingroup$ 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. $\endgroup$– acvillCommented 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__ ♦Commented Feb 2, 2022 at 18:57
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1$\begingroup$ I did not know you could download all the search results at once as fasta. $\endgroup$ Commented Feb 4, 2022 at 14:07
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How about trying this?
- 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]
