Question: Where can i get virus nt database for blastn?
0
gravatar for yashwanthakumar
2.0 years ago by
yashwanthakumar10 wrote:

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.

virus blastn nt database genome • 841 views
ADD COMMENTlink written 2.0 years ago by yashwanthakumar10
0
gravatar for shenwei356
2.0 years ago by
shenwei3565.5k
China
shenwei3565.5k wrote:

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

ADD COMMENTlink written 2.0 years ago by shenwei3565.5k
1

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 REPLYlink modified 2.0 years ago • written 2.0 years ago by genomax91k

Is it also applicable in nt datebase?

ADD REPLYlink written 5 months ago by liqi12020

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 REPLYlink written 5 months ago by genomax91k
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