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Archiver > GENEALOGY-DNA > 2007-08 > 1187928937
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Subject: Re: [DNA] Does Ian's tool extract mutations from sequences thatdon't have contr
Date: Fri, 24 Aug 2007 00:15:37 EDT
>If so, how does one ascertain whether Herrnstadt's sequences contain the
>control region - that is, without learning to recite the entire control
>sequence from memory.
OK, I can understand your frustration because it is not easy.
I am just trying to get people to study the techniques because
you learn more by doing it yourself and looking at the results
when you see an mtDNA report.
When you get a blast result, click on the accession number or:
Go to
_http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide&cmd=search&term_
(http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide&cmd=search&term) =
Then enter one of the accession numbers you already know,
EF657289 from Herrnstadt.
You will only see one report come up as CoreNucleotide records.
Click on it.
If it is the completed report, it will show authors, journal
articles etc.
Scroll down to the bottom of the results.
Note that the nucleotides end with
number 15446 or so.
You were interested in knowing whether
this person had 16235, 16291, 16293 and
16400 mutations. Those numbers are not
there at all, so it looks like the HVR1 was
not reported, correct? You basically need to
just know that the HVR2 are numbers at the
beginning of the report, and HVR1 are numbers
at the end. If you see numbers in the sequence
missing, then you know the sequence is incomplete
even if the title says it is complete.
Most complete mitochondria will have about
16569 or more base pairs listed.
Ian tries to determine the haplogroup and
subhaplogroups whenever possible.
Hope this helps!
Kathy J.
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