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Is it possible to BLAST against all SRA database?

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 ?

sequencing sra data blast genomic
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written by user3425664 • user3425664

2 answers

Maybe, this paper might be interesting: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001421

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written by colindaven colindaven

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.

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written by GenoMax GenoMax

Thanks, I'm aware of this option, the only problem is that you have to specify what you want to blast against.

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written by user3425664 • user3425664

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?

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written by GenoMax GenoMax

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.

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written by user3425664 • user3425664

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