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How to get BLAST wgs database

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
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updated by GenoMax GenoMax • written by Michael Michael

1 answer

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.

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written by GenoMax GenoMax

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?

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written by Michael Michael

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 :-)

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written by GenoMax GenoMax

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