command line Ncbi Blast SRA remote

Question

[acx01c]

I am willing to make a bunch of blast queries in ncbi hosted SRA datasets.

The blast query is fast, I want to search for two short sequences X and Y in SARS-CoV-2 datasets, Y is a mutated version of X, and stop when 100 reads are found, in order to find if sometimes Y appears as a minority variant of X, and conversely.

It seems this is not allowed (anymore?), neither by the blast Web API nor by the blastn command line executable.

So this fails blastn -db SRX10000025 -query XY.fasta -remote -out blast_output.out as well as github/srablast and blast/Web API.

On the other hand the blast interface allows to do it for one SRA.

Is there any way to get over this?

[acx01c]

I made a demo there showing that ncbi is blocking SRA requests outside of the Web interface:

http://cov2.infinityfreeapp.com/blast.html nt request, works

http://cov2.infinityfreeapp.com/blast_sra.html SRA request, is blocked.

[acx01c]

Sometimes the SRA request works too, but more frequently it fails with

Non-interactive SRA BLAST searches not supported. User IP address: 235.175.46.207

Answer 1

[GenoMax]

NCBI moved SRA database into amazon/google cloud last year. That may be one of the reasons why one can't do a remote blast against entries in SRA database.

NCBI's blast web application is likely using a private link to enable web based SRA blast searches.

[acx01c]

Clearly blasting SRA is more computationally expensive, no it is natural that there are some restrictions, but I don't understand what ncbi is wanting me to do. Ncbi mentions blasting on the amazon cloud but I don't understand how it works. I think I am just going to make a chrome extension faking to be clicking on the buttons of the web interface..

(by the way some SRA seem to lack a blast DB, we can see the reads but not blast. A blast DB is just the list of the 8-letters words and where they are appearing in the NGS data?)

[GenoMax]

This does come with a risk that NCBI may flag your IP and your computer may be banned from using web blast.

NCBI makes a special database available for SARS-CoV-2 data (LINK, look under BLAST_DB). Perhaps you can download that database and use it locally.