Answers.Body: <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>
  
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Answers.CreationDate: 2022-02-22T18:40:35.357Z
Answers.LastActivityDate: 2022-02-22T18:40:35.357Z
Answers.UserDisplayName: M__
Answers.Body: <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>
  
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Answers.UserDisplayName: Supertech
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-23T09:29:00.283Z
Comments.Text: 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.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-23T10:17:23.167Z
Comments.Text: 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
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-23T11:04:43.560Z
Comments.Text: Thanks for the help. Is it normal for the results to appear in the form o html?
Comments.UserDisplayName: Sofia
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-23T13:06:59.843Z
Comments.Text: You are referring to results of Entrez.read(handle) ? It's a something like a dictionary. You can check with type(record)
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-28T05:15:31.077Z
Comments.Text: @StupidWolf I concur: I also only see COI.  There are no 'cytb' sequences for this species, and that is why you get 0 hits.
Comments.UserDisplayName: user3479780
Tags: <database><nucleotide-models><efetch>
Title: Extracting a cytochrome B sequence from NCBI's nucleotide database
ThreadText: # 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**: @username_2 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](https://www.ncbi.nlm.nih.gov/nuccore/MZ571562.1)
  
  ```
   ... 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.
  
  
  ---
  
  