Remote blast of SRA database

Question

[emre.cto]

I am trying to use blast remotely using command line. I want to specify a certain database to blast, and I figured it out for WGS databases:

./blastn -db WGS_VDB://EXAMPLEID01 -query tmp.fa -out out.txt -remote

However, I don't know how to do it for SRA databases. Since it is possible to do it manually using the web interface, I figured that it should be possible to do it if I can specify the correct db name for the given SRA experiment.

Does anyone know how to do it and can provide an example?

Thanks!

Answer 1

[Brice Sarver]

The SRA-searching blastn is part of sra-tools.

Check out the blastn README on sra-tools' Github. Note that the SRA objects are prefetched.

[emre.cto]

This solved my problem, thanks!