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Old 1st December 2016, 06:03 PM
FredH FredH is offline
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Mt-DNA FASTA File Structure

Hello, I tried to read my MT-DNA Fasta File. It 's a text file then it should be easy except I didn't find the right mutation at the right place also the number of the Character is 16577, it 's little bit more than expected , I expected 16569 character, each corresponding to a base pair. Then I wonder what is it inside this file? and how to read it. The header countains > myftdnanumber,HVR2,CR,HVR1.
Any Ideas?
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Old 2nd December 2016, 09:37 AM
Ann Turner Ann Turner is offline
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The FASTA file is yourspecific sequence. If you have insertions (or deletions) compared to the CRS, that will throw the alignment off if you're simply counting bases. Utilities that analyze FASTA files will take those indels into account and get back on track. You can upload a FASTA file to James Lick's tool:

http://dna.jameslick.com/mthap/
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Old 2nd December 2016, 03:23 PM
FredH FredH is offline
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Quote:
Originally Posted by Ann Turner View Post
The FASTA file is yourspecific sequence. If you have insertions (or deletions) compared to the CRS, that will throw the alignment off if you're simply counting bases. Utilities that analyze FASTA files will take those indels into account and get back on track. You can upload a FASTA file to James Lick's tool:

http://dna.jameslick.com/mthap/
Thank, I didn't know about this problem. How do I know that there are insertions (or deletions)? We have to do a kind of alignment with the reference? Extracting info from Fasta is not so straight forward, then.

Last edited by FredH; 2nd December 2016 at 03:28 PM.
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Old 2nd December 2016, 07:27 PM
Ann Turner Ann Turner is offline
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Quote:
Originally Posted by FredH View Post
Thank, I didn't know about this problem. How do I know that there are insertions (or deletions)? We have to do a kind of alignment with the reference? Extracting info from Fasta is not so straight forward, then.
Yes, it's tricky and tedious to extract the differences from the CRS. What is your goal? FTDNA does this for you, as does James Lick's utility and probably others that I don't happen to use.
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Old 3rd December 2016, 12:54 PM
FredH FredH is offline
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Quote:
Originally Posted by Ann Turner View Post
Yes, it's tricky and tedious to extract the differences from the CRS. What is your goal? FTDNA does this for you, as does James Lick's utility and probably others that I don't happen to use.
I downloaded my Fasta File to check some results and compare with others. I prefer to see the mutation directly from the raw files. But from the Fasta file it's not easy because there is no position information in fact. I prefer the Bam file. I enter the position and I see the mutation as I did on ancient DNA Bam file on MT-DNA with BamView program. I wonder if FTDNA could provide my Bam File for MT-DNA? Otherwise I found FASTA To RSRS.exe program which give me directly all the mutations from a Fasta File but with no more explanations.

Last edited by FredH; 3rd December 2016 at 12:59 PM.
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