Question: How to get BLAST wgs database
0
gravatar for qwertzio
9 months ago by
qwertzio0
qwertzio0 wrote:

I would like to "mimic" the online BLASTn wgs search (NOT nt, this works already) on my local machine. The reason is that I want to extend from the BLAST nt search to a broader range of bacterial strains.

It seems like there is no BLAST wgs database to download. How do I determine which genomes I have to download to catch the genomes in wgs. I only need it for bacteria for a start.

An alternative would be to not use the entire wgs but some method to at least "broaden" the search compared to BLAST nt.

blast wgs • 498 views
ADD COMMENTlink modified 9 months ago by genomax77k • written 9 months ago by qwertzio0
2
gravatar for genomax
9 months ago by
genomax77k
United States
genomax77k wrote:

Did you take a look at this README file NCBI provides for instructions on how to deal with WGS data with blast+? Scripts you need are in this directory. Bacteria are taxid 2.

ADD COMMENTlink modified 9 months ago • written 9 months ago by genomax77k

That's really cool! This means that the data is first downloaded to the local machine to execute the search, right? So the search is not performed on NCBI servers?

ADD REPLYlink written 9 months ago by qwertzio0

You should check that by using a specific bacterial taxid first (e.g. Pseudomonas etc). If the data is downloaded locally then you had better have access to plenty of local storage :-)

ADD REPLYlink written 9 months ago by genomax77k
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