GENEALOGY-DNA-L Archives
Archiver > GENEALOGY-DNA > 2007-10 > 1192376881
From:
Subject: Re: [DNA] FGS posting on Mitosearch
Date: Sun, 14 Oct 2007 11:48:01 EDT
In a message dated 10/14/2007 5:47:31 AM Pacific Daylight Time,
writes:
> I do hope that some one answers this part of the query. I am also
> confused. I don't even know if I am suppose to be able to compare
> them to others. I sent mine in and I know that they are included for
> I saw Ian note with my identification number listed and I did look to
> see if they were correct.
Yes, you can compare your sequence with others in the GenBank database,
although it requires using some specialized bioinformatics tools. Linda Jonas wrote
up some detailed instructions:
http://archiver.rootsweb.com/th/read/genealogy-dna/2007-02/1171046241
If you just want a quick answer about your closest matches, stop at this
instruction:
> 5. You will now see the “results of BLAST” page. Scroll down the page.
> Your sequence will be at the top of the results list, with your closest matches
> below.
If you have any perfect matches, they'll show as 100% in the "Max ident"
column. Click on the hyperlinks in the "Accession" column to see the source of
that sequence.
You will probably see a very large number of sequences with 99% "Max ident,"
because most mtDNA sequences (maybe even all) will match on that many markers.
However, the list is sorted so that the closest matches are at the top. Click
on the "Max score" hyperlink for your next closest match to see how close it
actually is in absolute terms. For instance, it might say "Identities =
16565/16570." That would mean that you differ at five locations, so you wouldn't be
closely related to that sequence in genealogical terms.
I also encourage people to investigate the phylogenetic tree at MitoMap,
which integrates sequence data from a large number of technical citations. It
takes a lot of panning and zooming, but you'll get a better feel for your position
on the tree.
http://www.mitomap.org/mitomap-phylogeny.pdf
When I write custom reports for people, I redraw their section of the tree to
show how their sequence would modify it. The tree has not been updated since
September of 2006, and I'm hoping the next edition will include the personal
sequences that have been submitted to GenBank. At least the designers expressed
some interest when I wrote to them about it (unlike mtDB, where Max Ingman
expressly said he only wanted collections of sequences from defined geographical
locations).
Ann Turner
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