Is it possible to obtain all bacterial assemblies from RefSeq and GenBank that contain a specific gene?
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7 months ago
Bhargava • 0

Hello,

I am trying to do some analysis on bacterial assemblies containing a particular AMR gene. I tried searching through NCBI genbank, refseq and it does not give me all the assemblies. I tried blasting using web based blast with the accession for the gene. It keeps giving me error and the blast doesnt give me any results. Downloading all the bacterial assemblies from RefSeq and GenBank seems to be a foolish task with terabytes of space needed. I am not sure how efficient would it be. Can I blast against the databases which are hosted somewhere on cloud services to get results out of it?

Any suggestions or ideas on how to obtain these would be much appreciated. Thank you!

Genbank ncbi assemblies refseq bacteria • 899 views
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Do you need the whole genome, or just the gene representative?

I'd go through the BLAST protein or gene databases. You can get specific protein accession numbers, and its then possible to use Entrez to pull out related records like entire genomes etc.

You'll need to tell us what your BLAST error is for us to be able to help.

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This is how the error pops up

I think it's because I am selecting to get all matches - upto 5000 sequences (since I do not know how many matches are there) then, I am also searching in the whole RefSeq_genome database for all bacteria - think this is causing the error because the query is just too big of a job.

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I don't think that's the issue - BLAST will return thousands of results quite easily.

For some reason your sequences are not returning any significant hits. Have you tried just doing a generic BLAST with your query without specifying any filters?

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Would you mind pointing me in the direction of how to use Entrez to pull out the assemblies that contain this gene? Yes, I do no need the whole assemblies for my analyses.

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