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Where can i get virus nt database for blastn?

I have human genome samples and I want to find any bacterial or viral integration with my genome. But I couldnt find any nt database for virus.

genome virus nt blastn database
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written by yashwanthakumar • yashwanthakumar

1 answer

follow this https://bioinf.shenwei.me/taxonkit/tutorial/

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written by shenwei356 shenwei356

Viruses (top level including everything) have taxID: 10239.

If you need to restrict to a specific subset of viruses then use the NCBI Taxonomy browser to identify the taxID you would want to use with @shenwei's tutorial.

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written by GenoMax GenoMax

Is it also applicable in nt datebase?

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written by liqi1202 • liqi1202

If you are using a local copy of nt database for blast+ it is now simple to do with a new option -taxids. This allows you to limit results to only those taxID.

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written by GenoMax GenoMax

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