Answers.Body: <p>Hmmm, I am not experienced enough in biology or bioinformatics to truly understand the question, but I am guessing you want to download the FASTA file or genebank file containing the sequence of the accession number you listed above.
  There are 2 ways to do this -</p>
  <ol>
  <li>Using your browser, if you want to download a small sample of files. On the right hand side of your screen you can see the &quot;send to&quot; button on this link, click on it and choose the what's appropriate for you and then click on create file.</li>
  </ol>
  <p><code>https://www.ncbi.nlm.nih.gov/nuccore/MT742594.1</code></p>
  <ol start="2">
  <li><p>If you familiar with Biopython and python programming you can download multiple files at once in whatever format you want, there is an easy script to do this and has been taken from Biopython's documentation on biopython.org</p>
  <p>import os</p>
  <p>from Bio import SeqIO</p>
  <p>from Bio import Entrez</p>
  <p>Entrez.email = &quot;A.N.Other@example.com&quot;  # Always tell NCBI who you are</p>
  <p>filename = &quot;MT742594.1.gb&quot;</p>
  <p>if not os.path.isfile(filename):</p>
  <pre><code> # Downloading...
  
   net_handle = Entrez.efetch(
  
       db=&quot;nucleotide&quot;, id=&quot;MG762674&quot;, rettype=&quot;gb&quot;, retmode=&quot;text&quot;
  
   )
   out_handle = open(filename, &quot;w&quot;)
  
   out_handle.write(net_handle.read())
  
   out_handle.close()
  
   net_handle.close()
  
   print(&quot;Saved&quot;)
  </code></pre>
  <p>print(&quot;Parsing...&quot;)</p>
  <p>record = SeqIO.read(filename, &quot;gb&quot;)</p>
  <p>print(record)</p>
  </li>
  </ol>
  <p>You can make a list of the accession numbers of the sequences you want to download and pass the list in the id, if you are curious as to how the code works visit biopython.org .</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-31T14:16:39.817Z
Answers.Text: I still cant figure out this code block thingy!!!
Answers.UserDisplayName: Neeleshwar Pandey
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-31T18:50:55.657Z
Answers.Text: The easiest thing to do is just wrap 3 ``` symbols before and after the code.
Answers.UserDisplayName: user438383
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-31T14:15:54.900Z
Answers.LastActivityDate: 2020-10-31T14:15:54.900Z
Answers.UserDisplayName: Neeleshwar Pandey
Body: <p>I seem to have landed on the <a href="https://www.mitomap.org/MITOMAP" rel="nofollow noreferrer">mitomap.org</a> site, but I don't know what to make of it or what do with it / how to get the genomes onto my computer. It sounds like the genomes are stored in GenBank, but that mitomap simply lists which of the GenBank genomes are human mitochondrial haplogroup genomes.</p>
  <p>First of all, I can't find a simple list of links or list of names of the haplogroups the mitomap has... Can you show me where I can get or download that? They say:</p>
  <blockquote>
  <p>This brings our total number of FL sequences to 51,673, and the number of CR sequences to 74,660. Our SNVs now total 19,227.</p>
  </blockquote>
  <p>I don't know what FL or CR (Control Region sequences?) means, but I am expecting to see lists of genomes or something. What am I to do with this information? Where do I find this data? Is <a href="https://www.ncbi.nlm.nih.gov/nuccore/?term=(015400%5BSLEN%5D%3A016700%5BSLEN%5D)+AND+Homo%5BOrganism%5D+AND+mitochondrion%5BFILT%5D+NOT+(unverified+OR+Homo+sp.+Altai+OR+Denisova+hominin+OR+neanderthalensis+OR+heidelbergensis+OR+consensus)" rel="nofollow noreferrer">this</a> it? If I click on one of the results, I see <a href="https://www.ncbi.nlm.nih.gov/nuccore/MT742594.1" rel="nofollow noreferrer">this</a>. It has path <code>nuccore/MT742594.1</code>, can I find this in some NCBI FTP server somewhere? I don't see anything of that folder structure in the <a href="https://ftp.ncbi.nlm.nih.gov/genbank/" rel="nofollow noreferrer">GenBank FTP server</a>...</p>
  <p>Basically my question is:</p>
  <ol>
  <li>Where is the complete list of human mitochondrial haplogroup genomes?</li>
  <li>Where can I download all of those human mitochondrial haplogroup genomes so I can get them onto my computer?</li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-31T20:24:33.970Z
Comments.Text: There is no such thing as "list of human mitochondrial haplogroup genomes". A haplogroup is not a genome but a list of variants common for many genomes.
Comments.UserDisplayName: juanjo75es
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-26T03:51:36.520Z
Comments.Text: Data is located here: https://www.mitomap.org/foswiki/bin/view/MITOMAP/Mitobank. Under the Sequences available column, you can download a text file containing genbank_id. You need to write a script to download all these files. My back of the envelope calculation suggest you will download about 1GB data. I suggest test few entry first.
Comments.UserDisplayName: Supertech
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-26T03:52:18.263Z
Comments.Text: Just realized this entry is very old :)
Comments.UserDisplayName: Supertech
Tags: <genome><data-download><public-dataset>
Title: How do I download the mitochondrial haplogroup datasets for human genetics online?
ThreadText: # How do I download the mitochondrial haplogroup datasets for human genetics online?
  
  (Asked by: username_0 on 2020-10-31)
  
  I seem to have landed on the [mitomap.org](https://www.mitomap.org/MITOMAP) site, but I don't know what to make of it or what do with it / how to get the genomes onto my computer. It sounds like the genomes are stored in GenBank, but that mitomap simply lists which of the GenBank genomes are human mitochondrial haplogroup genomes.
  
  First of all, I can't find a simple list of links or list of names of the haplogroups the mitomap has... Can you show me where I can get or download that? They say:
  
  > This brings our total number of FL sequences to 51,673, and the number of CR sequences to 74,660. Our SNVs now total 19,227.
  
  I don't know what FL or CR (Control Region sequences?) means, but I am expecting to see lists of genomes or something. What am I to do with this information? Where do I find this data? Is [this](https://www.ncbi.nlm.nih.gov/nuccore/?term=(015400%5BSLEN%5D%3A016700%5BSLEN%5D)+AND+Homo%5BOrganism%5D+AND+mitochondrion%5BFILT%5D+NOT+(unverified+OR+Homo+sp.+Altai+OR+Denisova+hominin+OR+neanderthalensis+OR+heidelbergensis+OR+consensus)) it? If I click on one of the results, I see [this](https://www.ncbi.nlm.nih.gov/nuccore/MT742594.1). It has path `nuccore/MT742594.1`, can I find this in some NCBI FTP server somewhere? I don't see anything of that folder structure in the [GenBank FTP server](https://ftp.ncbi.nlm.nih.gov/genbank/)...
  
  Basically my question is:
  
  1. Where is the complete list of human mitochondrial haplogroup genomes?
  2. Where can I download all of those human mitochondrial haplogroup genomes so I can get them onto my computer?
  
  **Tags:** genome, data-download, public-dataset
  
  > **Comments:**
  > **username_1**: There is no such thing as "list of human mitochondrial haplogroup genomes". A haplogroup is not a genome but a list of variants common for many genomes.  
  > **username_2**: Data is located here: https://www.mitomap.org/foswiki/bin/view/MITOMAP/Mitobank. Under the Sequences available column, you can download a text file containing genbank_id. You need to write a script to download all these files. My back of the envelope calculation suggest you will download about 1GB data. I suggest test few entry first.  
  > **username_2**: Just realized this entry is very old :)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2020-10-31. Score: 1
  
  Hmmm, I am not experienced enough in biology or bioinformatics to truly understand the question, but I am guessing you want to download the FASTA file or genebank file containing the sequence of the accession number you listed above.
  There are 2 ways to do this -
  
  1. Using your browser, if you want to download a small sample of files. On the right hand side of your screen you can see the "send to" button on this link, click on it and choose the what's appropriate for you and then click on create file.
  
  `https://www.ncbi.nlm.nih.gov/nuccore/MT742594.1`
  
  2. If you familiar with Biopython and python programming you can download multiple files at once in whatever format you want, there is an easy script to do this and has been taken from Biopython's documentation on biopython.org
  
     import os
  
     from Bio import SeqIO
  
     from Bio import Entrez
  
     Entrez.email = "A.N.Other@example.com" # Always tell NCBI who you are
  
     filename = "MT742594.1.gb"
  
     if not os.path.isfile(filename):
  
     ```
      # Downloading...
  
      net_handle = Entrez.efetch(
  
          db="nucleotide", id="MG762674", rettype="gb", retmode="text"
  
      )
      out_handle = open(filename, "w")
  
      out_handle.write(net_handle.read())
  
      out_handle.close()
  
      net_handle.close()
  
      print("Saved")
  
     ```
  
     print("Parsing...")
  
     record = SeqIO.read(filename, "gb")
  
     print(record)
  
  You can make a list of the accession numbers of the sequences you want to download and pass the list in the id, if you are curious as to how the code works visit biopython.org .
  
  > **Comments:**
  > **username_3**: I still cant figure out this code block thingy!!!  
  > **username_4**: The easiest thing to do is just wrap 3 ``` symbols before and after the code.  
  
  ---
  
  