Retrieve certain gene from different WGS from NCBI

Question

[Trinh]

Dear colleagues,

I found 1 SNP in my favorite gene from WGS data on a pathogen. I want to check the frequency of these SNPs in other clinical isolates. I found that NCBI-BioSamples has around 100 WGS from different strains were published. Do you know if I can retrieve just the sequence of target genes I like?

It will be a lot of work if I run alignment again for 100 WGS strains. I hope there is some simple way.

Thank you very much for your help!

Answer 1

[GenoMax]

WGS sequences may be in varying stages of "completeness" so it is possible that one can't simply retrieve a specific gene using a name. NCBI web blast does allow you to search against the WGS database. You can further limit your search by adding the name of the organism you are working with.

[Trinh]

Ohm, Thank you very much!