GENEALOGY-DNA-L ArchivesArchiver > GENEALOGY-DNA > 2007-08 > 1187873704
Subject: Re: [DNA] How do you find your mutation list on FTDNA's (nowCRSdifferences)
Date: Thu, 23 Aug 2007 08:55:04 EDT
>In terms of interesting... When you search FGSs at GenBank those that
>match you completely or almost completely on the coding region are
>going to be more interesting than those that match you on HVR1. To
>draw a VERY rough comparison it is more important that two yDNA
>samples both be R1a than that they both have DYS390 equal.
>On 8/20/07, <> wrote:
>> My H2a2 full sequence (not a CRS) currently does not match
>> anybody at GenBank, but if you just enter the HVR1, you will
>> get many interesting matches, mostly from Scotland.? So it really
>> depends on if you query the full sequence or just a partial
>> sequence.?It is best not to enter too much or too little data
>> if you want to get a lot of matches, just copy and paste the
>> sequences that are of interest.
Yes, you are correct so let me clarify where I was going with my statement.
I only said "interesting" in this case because I wanted a sizable
number of geographically interesting results to pop up that
point to a specific journal article to show Dora how to use
partial sequences to find new information...
To show how to get my specific SNP to show up, which to
most people would be much more interesting because it is in the
coding region, then I should have entered the following sequence,
which is also a way to get Herrnstadt's data to come up again at
GenBank answering Dora's other question:
3361 ttcctaatgc ttaccgaacg aaaaattata ggctatatac aactacgcaa aggccccaac
where I have used a sequence from the CRS, changed 3388c to 3388a
which is a transversion instead of a transition by the way. Transversion
SNPs are great because the chance of homoplasy is so low that I
can assume it won't show up in another haplogroup.
If you enter too much information and make the sequence too long,
then Herrnstadt's results might be missed because it does not include
the HVR1. So why does GenBank title it "complete genome" when it
is in no way complete? Herrnstadt completely misses the important
HVR1 associations...NCBI titles can just drive you nuts sometimes.
Complete is not complete and haplotypes are not haplotypes...
And this is supposed to be THE standard by which we compare???
In my last e-mail there was a typo, it should have read 437 instead
of the "first 427 sequences of the CRS" define the SMGF HVR2.
Too much jet lag.
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