Extracting a cytochrome B sequence from NCBI's nucleotide database

Question

Can someone tell the way to extract the fasta sequences for the gene cytb of Acetes japonicus (shrimp important to China and South Korea)?

Can I extract them directly from NCBI nucleotide database (i.e. nuccore)?

For instance, I'm trying to fetch the fasta data of Acetes japonicus of cytb gene. So I'm using biopython, like this:

 handle = Entrez.esearch(db="nucleotide", term="Acetes japonicus[Orgn] AND cytb[Gene]")
record=Entrez.read(handle)

And the output doesn't give the an ID, however when I search manually I get the result.

What sequences? The gene? The CDS? The various spliced transcripts? Protein? In what species? Please edit and make your question more specific and we can give you specific answers. — terdon, Oct 23, 2019 at 9:29
Weird, when I search the nucleotide database, I see only COI gene. You can try handle = Entrez.esearch(db="nucleotide", term="Acetes japonicus[Orgn] AND COI[Gene]",idtype="acc") and you will see that it works. Substitute COI for cytb and it's empty. Exactly what I saw in entrez nucleotide database — StupidWolf, Oct 23, 2019 at 10:17
Thanks for the help. Is it normal for the results to appear in the form o html? — Sofia, Oct 23, 2019 at 11:04
You are referring to results of Entrez.read(handle) ? It's a something like a dictionary. You can check with type(record) — StupidWolf, Oct 23, 2019 at 13:06
@StupidWolf I concur: I also only see COI. There are no 'cytb' sequences for this species, and that is why you get 0 hits. — user3479780, Oct 28, 2019 at 5:15

M__ · Accepted Answer · 2022-02-22 18:40:35Z

I should have answered correctly ages back, because I do know it.

Cytochrome b is a massively used target for arthropods - these are shrimps. However, the nomenclature changed:

Wait you might ask, arn't you confusing that with COI, II, III? No because that nomenclature changed too:

'New' was a long time ago though.

Thus the gene you are looking for is MZ571562, here

 ... AND COB [gene]

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