Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-16T18:19:31.763Z
Answers.Text: That's great, thank you very much. I've one more question, I'm also working with ancient mitochondrial sequences in which there is no such reference sequence, what do you suggest for them?
Answers.UserDisplayName: iamakhilverma
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-16T18:23:00.637Z
Answers.Text: Also, which aligner would you recommend for this purpose?
Answers.UserDisplayName: iamakhilverma
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-16T19:38:21.350Z
Answers.Text: @AkhilVerma sorry, I don't know anything about ancient sequences. If they're hominid, I would still try the same approach, but I've never worked with mitochondria so I don't know what level of conservation you can expect. Still worth a try, though. As for the aligner, any should do. These will all be very similar sequences, in principle, so not a hard problem. Since they're relatively long, I would personally go for `mafft`, but I doubt it would make much difference.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-16T21:21:51.823Z
Answers.Text: Again, Thank you so much for your help.
Answers.UserDisplayName: iamakhilverma
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-16T17:53:56.977Z
Answers.LastActivityDate: 2019-11-16T17:53:56.977Z
Answers.UserDisplayName: terdon
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-16T16:45:37.933Z
Comments.Text: Do you have the target coordinates?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-16T17:02:54.553Z
Comments.Text: No, I don't. actually, I read about it and found out that hypervariable regions(HVR) 1,2, 3 have target coordinates and I suppose they will differ in each of my files downloaded from GenBank and when I checked, there was no such information in GenBank regarding that. What should I do now? Is there any other way possible? I thought it might be pretty standard thing to extract hypervariable region from Mito DNA.
Comments.UserDisplayName: iamakhilverma
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-16T17:24:00.023Z
Comments.Text: Please [edit] your question and add some more information. Show us the sequences you have, and most especially tell us what species you're working with. I imagine you've tried simply googling for "mitochondrial hypervariable regions" or searching PubMed etc, right? Didn't that bring you anything helpful?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-16T17:40:06.390Z
Comments.Text: yes, I have done those google searches already and no, it didn't answer my questions. Searching for HVRs coordinates and then extracting them one by one is what I gathered from the searches, but it will make it a very cumbersome task. I've edited my question, please see it.
Comments.UserDisplayName: iamakhilverma
Tags: <fasta><phylogenetics><database><phylogeny><genomics>
Title: How to extract hypervariable region of mitochondrial dna from its fasta file?
ThreadText: # How to extract hypervariable region of mitochondrial dna from its fasta file?
  
  (Asked by: username_0 on 2019-11-16)
  
  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](https://www.ncbi.nlm.nih.gov/nuccore/MK248274.1?report=fasta)
  
  **Tags:** fasta, phylogenetics, database, phylogeny, genomics
  
  > **Comments:**
  > **username_1**: Do you have the target coordinates?  
  > **username_0**: No, I don't. actually, I read about it and found out that hypervariable regions(HVR) 1,2, 3 have target coordinates and I suppose they will differ in each of my files downloaded from GenBank and when I checked, there was no such information in GenBank regarding that. What should I do now? Is there any other way possible? I thought it might be pretty standard thing to extract hypervariable region from Mito DNA.  
  > **username_1**: Please [edit] your question and add some more information. Show us the sequences you have, and most especially tell us what species you're working with. I imagine you've tried simply googling for "mitochondrial hypervariable regions" or searching PubMed etc, right? Didn't that bring you anything helpful?  
  > **username_0**: yes, I have done those google searches already and no, it didn't answer my questions. Searching for HVRs coordinates and then extracting them one by one is what I gathered from the searches, but it will make it a very cumbersome task. I've edited my question, please see it.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-11-16. Score: 2 | Accepted answer
  
  You can use [Mitomap](https://www.mitomap.org/) to get the coordinates of the hypervariable regions in the [rCRS mitochondrial sequence](https://www.ncbi.nlm.nih.gov/nuccore/251831106) (the standard MT sequence in the field). I checked the [Genome Loci](https://www.mitomap.org/foswiki/bin/view/MITOMAP/GenomeLoci) 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.
  
  > **Comments:**
  > **username_0**: That's great, thank you very much. I've one more question, I'm also working with ancient mitochondrial sequences in which there is no such reference sequence, what do you suggest for them?  
  > **username_0**: Also, which aligner would you recommend for this purpose?  
  > **username_1**: @AkhilVerma sorry, I don't know anything about ancient sequences. If they're hominid, I would still try the same approach, but I've never worked with mitochondria so I don't know what level of conservation you can expect. Still worth a try, though. As for the aligner, any should do. These will all be very similar sequences, in principle, so not a hard problem. Since they're relatively long, I would personally go for `mafft`, but I doubt it would make much difference.  
  > **username_0**: Again, Thank you so much for your help.  
  
  ---
  
  