I would like to blast a short nt sequence around 245 nt, is it possible to somehow blast against all genomic sequencing run data on SRA ?
Maybe, this paper might be interesting: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001421
Blasting against SRA is only possible via Blast web interface: https://blast.ncbi.nlm.nih.gov Choose "SRA" as target database in database options. I don't think you can limit the search to just genomic sequences.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
Thanks, I'm aware of this option, the only problem is that you have to specify what you want to blast against.
There is no other option, unless you download whatever you need/want from SRA locally and build a database. A theoretically possible task but practically impossible :-)
What is the use case here? What does that query sequence contain?
I'm trying to find a specific mutation of the SARS-CoV2 genome. I want to be able to scan for it in SRA reads to see if a consensus was made against it.