text: user2883: Recently I've done some analysis on human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed are linked to only hypervariable regions. To do that, I'll need to make new fasta files from the mitochondrial DNA entries that I have and I want to know how to extract those. Any leads will be appreciated.
  Link to one of the reference fasta files that I have
  
  user298: You can use Mitomap to get the coordinates of the hypervariable regions in the rCRS mitochondrial sequence (the standard MT sequence in the field). I checked the Genome Loci section of Mitomap and saw that it lists three:
  Map Locus   Starting    Ending  Shorthand   Description
  MT-HV1      16024       16383   CR:HVS1/HV1 Hypervariable segment 1 
                                              [classic:16024-16365]
  MT-HV2      57          372     CR:HVS2     Hypervariable segment 2
                                              [classic:73-340 ]   
  MT-HV3      438         574     CR:HVS3     Hypervariable segment 3
  
  That gives you the coordinates on the rCRS sequence. What you can do now, is align all of your sequences and the rCRS together and see if you can infer where the hypervariable regions fall in your target sequences. Since, presumably, the rest of the sequence will be more conserved since it isn't hypervariable, you should be able to identify the syntenic blocks and locate the hypervariable regions in your sequences. I would expect to see a very high level of sequence identity in the non-hypervariable regions across all of your sequences (since they're all human mitochondria), so you should be able to find the hypervariable ones as the regions of low sequence similarity which also coincide with the known coordinates of the rCRS.
  
original_text: 2883: <p>Recently I've done some analysis on human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed are linked to only hypervariable regions. To do that, I'll need to make new fasta files from the mitochondrial DNA entries that I have and I want to know how to extract those. Any leads will be appreciated.</p>
  
  <p><a href="https://www.ncbi.nlm.nih.gov/nuccore/MK248274.1?report=fasta" rel="nofollow noreferrer">Link to one of the reference fasta files that I have</a></p>
   298: <p>You can use <a href="https://www.mitomap.org/" rel="nofollow noreferrer">Mitomap</a> to get the coordinates of the hypervariable regions in the <a href="https://www.ncbi.nlm.nih.gov/nuccore/251831106" rel="nofollow noreferrer">rCRS mitochondrial sequence</a> (the standard MT sequence in the field). I checked the <a href="https://www.mitomap.org/foswiki/bin/view/MITOMAP/GenomeLoci" rel="nofollow noreferrer">Genome Loci</a> section of Mitomap and saw that it lists three:</p>
  
  <pre><code>Map Locus   Starting    Ending  Shorthand   Description
  MT-HV1      16024       16383   CR:HVS1/HV1 Hypervariable segment 1 
                                              [classic:16024-16365]
  MT-HV2      57          372     CR:HVS2     Hypervariable segment 2
                                              [classic:73-340 ]   
  MT-HV3      438         574     CR:HVS3     Hypervariable segment 3
  </code></pre>
  
  <p>That gives you the coordinates on the rCRS sequence. What you can do now, is align all of your sequences and the rCRS together and see if you can infer where the hypervariable regions fall in your target sequences. Since, presumably, the rest of the sequence will be more conserved since it isn't hypervariable, you should be able to identify the syntenic blocks and locate the hypervariable regions in your sequences. I would expect to see a very high level of sequence identity in the non-hypervariable regions across all of your sequences (since they're all human mitochondria), so you should be able to find the hypervariable ones as the regions of low sequence similarity which also coincide with the known coordinates of the rCRS.</p>
  