GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2010-11 > 1290527007


From: Ann Turner <>
Subject: Re: [DNA] Searching GenBank ?
Date: Tue, 23 Nov 2010 07:43:27 -0800
References: <924930.16872.qm@web33406.mail.mud.yahoo.com>
In-Reply-To: <924930.16872.qm@web33406.mail.mud.yahoo.com>


The FASTA download is now in the mtDNA tab on the left, under "Print
Certificate / Report Data."

When I write custom reports, I follow up with tailored instructions on how
to search using their GenBank ID instead of the FASTA file. Sometimes the
generic method doesn't give the best result.

Here are some instructions I posted about a year ago -- they still look OK:

=====

The FASTA files at FTDNA used to be in HVR1-HVR2-CR order (i.e. not in
numerical order). I just now noticed that they are now correct, so they can
be
used to check GenBank for your closest matches.

Go to http://www.ncbi.nlm.nih.gov/blast/ and click on "nucleotide blast."

In the box labeled "Enter Query Sequence" paste your FASTA file.

In the box labeled "Choose Search Set" click on the radio button by "Others
(nr etc.)"

In the box labeled "Program Selection" click on the radio button by "Highly
similar sequences (megablast)".

Then click on the BLAST button at the bottom of the page. The search may
take a few minutes to display your matches, with the closest at the top.
Scroll down to the table that has hyperlinks for Accession and Max Score.

Click on the Max Score hyperlink. It takes you down to the part of the page
with details about the alignment. The places where you don't match lack the
vertical bar | but that's not a particularly useful way to view the data.
The numbers in the left-hand margin won't necessarily match the CRS numbers
due to insertions / deletions.

However, you can see that there are several gaps in the alignment if you
search for | | (the vertical "pipe" symbol above the \ on your keyboard,
then
a space, then | again). If you want to see that record's list of differences
from the CRS, enter the GenBank ID at Ian Logan's "Checker" site,
http://www.ianlogan.co.uk/checker/genbank.htm . The GenBank ID is embedded
in the
Accession column: it has two letters, followed by six numbers.

The alignment section repeats the hyperlink for the Accession. Clicking on
that takes you to the GenBank record. If the record refers to a technical
article, you can click on the PubMed link to view the abstract of the
article.
Some of the articles have links to free full text.

You can continue to view your next closest matches in a similar fashion.
You can make it a point to check back every few months for new records.
Ideally, you'd like to find cases with just one (or maybe two) differences
from
your sequence for genealogical purposes. You can also see if a geographical
trend develops, but be cautious: the samples are usually not randomly
collected, but reflect the residence of the researcher!

Ann Turner


On Tue, Nov 23, 2010 at 7:24 AM, Peter J. Roberts <>wrote:

> Do you have simple step by step instructions for searching full sequence
> human
> mtDNA at GenBank?
>
>
> How do you download your full sequence mtDNA from FamilyTreeDNA in the
> FASTA
> format? In the past there was a link but I don't see it now. Yesterday I
> e-mailed FTDNA that question but I've not yet received a reply.
>
> Thanks and sincerely, Peter
>
> Peter J. Roberts
>


This thread: