Thursday, November 27, 2008

Journal of Genetic Genealogy

Fall Issue of the Journal of Genetic Genealogy

A few good articles in this season's edition of the Journal of Genetic Genealogy.

Those of you who are familiar with the DNA testing might recognize Whit Athey's name, he was the one to create the "Haplotype Predictor" (link found in the HAM Country DNA Tools area). Whit is the main editor of this "Journal of Genetic Genealogy."

Mentioned this month in JoGG is an interview with John Butler. You folks may not recognize him, but I had written him when I was first developing my program "ft2dna." John Butler is with NIST, the National Institute of Standards and Technology.

NIST keeps a catalog of Y-STR standards on their web site. I was converting FTDNA numbers into "ATGC" format a few years back, and many of the Y-STR markers were not yet posted to the internet. I wrote John Butler about it, and he was able to post the standards for all of the first 37 Y-STR markers tested from FTDNA. So, thanks to John Butler, I was able to complete the "ft2dna" program. (It is found in the "Tools" area of HAM Country).

Which, of course I used in the Lamarc mutation rate study for HAM DNA Group #2. (The bottom link on the main DNA Project page at HAM Country).

Funny thing, this past week I have been working on improvements to my "ft2dna" program, so that I can automate some of the work involved in running Lamarc (or PHYLIP) against our DNA groups. I have automated the "ft2dna" program sufficiently to generate a Genetic Distance chart of our entire project, as well as generate ATGC format for the entire HAM DNA Project these days. However, I have a number of bug fixes yet to complete, and I want to have the "ft2dna" program generate the results in the Lamarc file format (xml) for me. That could save me a considerable amount of time.

I have modified the "ft2dna" program to generate a "Dean McGee web page style" of a Genetic Distance chart, using the data that I use as input to Dean McGee's utility anyways. If you have downloaded the older version of the "ft2dna" program, the documentation has some links to NIST that I used as a reference to generate the "ATGC" format. Pretty grueling stuff to try to figure out on your own. For example, Sorenson uses DNA complements, which can be confusing if you are not aware of what they are doing. With a number of Y-DNA testing companies analyzing Y-STR values with different techniques, it becomes important to have a standard to apply for DNA Project administrators.

Butler has a PDF file in this issue of JoGG that shows the ATGC structure for Y-STR's that I was attempting to convert with the "ft2dna" program. A good reference if you are interested in how that conversion is done.

Ann Turner is on the Editorial Board at JOGG, and she helped me to figure out "how to" do the BLAST searches for the Y-STR values. I did those BLAST searches in order to verify that I was writing the "ft2na" program against reality. Ann Turner has also written a "Mutation Rate Calculator" also found in the DNA Tools area at HAM Country. She is also an expert at mtDNA, and has helped a number of Genetic Genealogy Project Administrators with their mtDNA analysis.

Anyways, it is good to see a standard from these Y-DNA testing companies. John Butler is interviewed in this season's issue of JOGG.


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