<p>I should have answered correctly ages back, because I do know it.</p>
<p>Cytochrome b is a massively used target for arthropods - these are shrimps. However, the nomenclature changed:</p>
<ul>
<li>Traditionally nomenclature <code>cytb</code></li>
<li>'New' nomenclature <code>COB</code></li>
</ul>
<p>Wait you might ask, arn't you confusing that with COI, II, III?  No because that nomenclature changed too:</p>
<ul>
<li>Traditional nomenclature <code>COI</code></li>
<li>'New' nomenclature <code>COX1</code></li>
</ul>
<p>'New' was a long time ago though.</p>
<p>Thus the gene you are looking for is MZ571562, <a href="https://www.ncbi.nlm.nih.gov/nuccore/MZ571562.1" rel="nofollow noreferrer">here</a></p>
<pre><code> ... AND COB [gene] 
</code></pre>

CC BY-SA 4.0
2022-02-22T18:40:35.357Z
2022-02-22T18:40:35.357Z
M__
<p>Here is how you can do it from command line version:</p>
<pre><code>esearch -db nuccore -query &quot;COB [GENE] AND &quot;Acetes japonicus&quot; [ORGN]&quot;|efetch -format gb
</code></pre>
<p>OR</p>
<pre><code>esearch -db nuccore -query &quot;COB [GENE] AND &quot;Acetes japonicus&quot; [ORGN]&quot;|efetch -format fasta
</code></pre>
<p>Note that gene name is actually COB.</p>

CC BY-SA 4.0
2024-03-14T02:52:03.013Z
2024-03-14T02:52:03.013Z
Supertech
<p>Can someone tell the way to extract the fasta sequences for the gene cytb of <em>Acetes japonicus</em> (shrimp important to China and South Korea)?</p>
<p>Can I extract them directly from NCBI nucleotide database (i.e. nuccore)?</p>
<p>For instance, I'm trying to fetch the fasta data of <em>Acetes japonicus</em> of cytb gene. So I'm using biopython, like this:</p>
<pre><code> handle = Entrez.esearch(db=&quot;nucleotide&quot;, term=&quot;Acetes japonicus[Orgn] AND cytb[Gene]&quot;)
record=Entrez.read(handle)
</code></pre>
<p>And the output doesn't give the an ID, however when I search manually I get the result.</p>

CC BY-SA 4.0
2019-10-23T09:29:00.283Z
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
CC BY-SA 4.0
2019-10-23T10:17:23.167Z
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
CC BY-SA 4.0
2019-10-23T11:04:43.560Z
Thanks for the help. Is it normal for the results to appear in the form o html?
Sofia
CC BY-SA 4.0
2019-10-23T13:06:59.843Z
You are referring to results of Entrez.read(handle) ? It's a something like a dictionary. You can check with type(record)
StupidWolf
CC BY-SA 4.0
2019-10-28T05:15:31.077Z
@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
<database><nucleotide-models><efetch>
Extracting a cytochrome B sequence from NCBI's nucleotide database
# Extracting a cytochrome B sequence from NCBI's nucleotide database

(Asked by: username_0 on 2019-10-23)

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.

**Tags:** database, nucleotide-models, efetch
> **Comments:**
> **username_1**: 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.  
> **username_2**: 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  
> **username_0**: Thanks for the help. Is it normal for the results to appear in the form o html?  
> **username_2**: You are referring to results of Entrez.read(handle) ? It's a something like a dictionary. You can check with type(record)  
> **username_3**: @StupidWolf I concur: I also only see COI.  There are no 'cytb' sequences for this species, and that is why you get 0 hits.  

---

## 2 answers

### Answer by username_4 on 2022-02-22. Score: 0

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:

Traditionally nomenclature cytb
'New' nomenclature COB

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

Traditional nomenclature COI
'New' nomenclature COX1

'New' was a long time ago though.
Thus the gene you are looking for is MZ571562, here
 ... AND COB [gene]


---

### Answer by username_5 on 2024-03-14. Score: 0

Here is how you can do it from command line version:
esearch -db nuccore -query "COB [GENE] AND "Acetes japonicus" [ORGN]"|efetch -format gb

OR
esearch -db nuccore -query "COB [GENE] AND "Acetes japonicus" [ORGN]"|efetch -format fasta

Note that gene name is actually COB.


---

