How can I query NCBI SRA for purpose of strain typing/profiling?

Question

[gatheringdusthere]

I read that one can search SRA database to retrieve sequence data from it and make comparisons with one's own sequencing reads. So if I found a strain of pathogenic E. coli, and I want to know if it is a totally new strain, other than initially blasting and mapping to reference genomes, I can search SRA to see if anyone else might be working on it or retrieve related data for comparison.

What I understand is that SRA is an archive of NGS data from ongoing projects which includes raw reads and draft assemblies. But I don't know how to use it or if what I am thinking of using it for is correct.

1. How do I compare my strain sequence read with those deposited in SRA, to see if there is a similar strain in there?

2. How do I even choose a experiment set to blast my sequence(s) against to begin with? Do I have to do a literature search to find relevant papers for SRA Experiment set (SRX) first?

Appreciate any direction on this topic.

Answer 1

[GenoMax]

There are 18000+ assemblies for E. coli in NCBI's genome database so it is unlikely that you have a totally new strain. You will likely have a strain that has differences compared to something that is already there.

Take a look at this page to see how you can blast search against SRA. I suggest that you limit your search using taxID for E. coli, which is 562.

[gatheringdusthere]

Thank you for the link to that page. I'll look through the different search strategies listed within.