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How to download/extract the same gene from all bacterial genomes on NCBI?

I would like to get all "groL" gene (nucleotide) sequences from all assembled bacterial genomes on NCBI. For example, searching for (groL) AND "bacteria"[porgn:__txid2] on NCBI Gene get's me a list of the sequences I want, but I seems like I have to open the links one by one to get the seqeuence, the "send to" menu only offers a list. I'd like to avoid sequence searches via BLAST to get this, as they should all be annotated well. Maybe there is a way via the e-utilities?

ncbi
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updated by GenoMax GenoMax • written by tbayer • tbayer

Unfortunately I need the sequences for a barcoding taxonomy db, so protein (or back-translations) won't help. Thanks!

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written by tbayer • tbayer

You may have to resort to blasting or perhaps simply back-translating the IPG sequences Mensur Dlakic mentioned below. As you probably saw, in the gene database while there is a list of groL entries not all of them have location information. That means we can't simply extract them based on location.

There may be a datasets way of doing this. Will try to see if I can test.

test

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written by GenoMax GenoMax

1 answer

So I decided instead of all bacterial genomes it was sufficient to have one per genus, which puts the number at a more manageable ~4k. I used rsync to download the *_cds_from_genomic.fna.gz files for all those from refeseq, and then seqkit grep -n -r -p gene=groL *.gz > groL_only.fasta to extract my gene of interest. The task that remains is to translate the genbank IDs from those sequences to the species, that should work with the e-utilities.

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written by tbayer • tbayer

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