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.
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$\begingroup$ Do you have the target coordinates? $\endgroup$– terdon ♦Nov 16, 2019 at 16:45
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$\begingroup$ 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. $\endgroup$– iamakhilvermaNov 16, 2019 at 17:02
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$\begingroup$ 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? $\endgroup$– terdon ♦Nov 16, 2019 at 17:24
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$\begingroup$ 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. $\endgroup$– iamakhilvermaNov 16, 2019 at 17:40
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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.
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$\begingroup$ 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? $\endgroup$ Nov 16, 2019 at 18:19
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$\begingroup$ Also, which aligner would you recommend for this purpose? $\endgroup$ Nov 16, 2019 at 18:23
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$\begingroup$ @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. $\endgroup$– terdon ♦Nov 16, 2019 at 19:38 -
$\begingroup$ Again, Thank you so much for your help. $\endgroup$ Nov 16, 2019 at 21:21