Question

Where can i get virus nt database for blastn?

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5.5 years ago

yashwanthakumar ▴ 10

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 • 1.9k views

ADD COMMENT • link 5.5 years ago by yashwanthakumar ▴ 10

score 0 · Answer 1 · 2018-10-26

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5.5 years ago

shenwei356 8.4k

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

ADD COMMENT • link 5.5 years ago by shenwei356 8.4k

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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.

ADD REPLY • link 5.5 years ago by GenoMax 141k

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Is it also applicable in nt datebase?

ADD REPLY • link 4.0 years ago by liqi1202 • 0

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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.

ADD REPLY • link 4.0 years ago by GenoMax 141k