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From: "RICHARD KENYON" <>
Subject: Re: [DNA] Question for Thomas Krahn - STRs in WOY regions
Date: Tue, 1 Jan 2008 20:49:55 -0800
References: <BAY111-DAV11D291540C53A47C5C4146BC510@phx.gbl><BAY103-DAV1394D6A53FB52649A029D7C8510@phx.gbl><1EFE90B9-6A1E-47D3-83DF-1D6B7A803E7E@vizachero.com>


The point I thought I was making that it is difficult to separate out the Y-chromosome from everything else so it could be sequenced. I was trying to say that this isolation of the Y-chromosome is the problem. I was not suggesting that a shotgun sequencing method (or any other) necessarily be used, as I think careful reading of what I said will show this.
However I might add, the whole genome project wouldn't have been completed ahead of schedule without using a shotgun approach to arrive at the first "draft" of the human genome. (The so-called "whole genome" is still only a "draft" and is incomplete with gaps and ambiguities, as I understand. So in a strict sense, this project has not been completed!).
The best description I've seen of the portion of the Y-chromosome we're most interested in is the article: "The Male-Specifiec Region of the Human Y Chromosome Is a Mosaic of Discrete Sequence Classes" by Helen Skaletsky et al (2003) that appeared in Nature, Vol. 423, 19 Jun 2003, pp. 825-837, plus supplementary information. It includes a map of the Y that can be enlarged for legibility (but it was somewhat challenging to get a hard copy).
Thanks for the link to the lecture PDF. The portion on bioinformatics was interesting.

Richard R. Kenyon ("Dick")
----- Original Message -----
From: Vincent Vizachero<mailto:>
To: <mailto:>
Sent: Tuesday, January 01, 2008 5:24 AM
Subject: Re: [DNA] Question for Thomas Krahn - STRs in WOY regions


Shotgun sequencing, for all its many advantages, does have real
disadvantages. Separating the Y-chromosome, which Ann mentioned, is
one of them. Shotgun sequencing is also not as accurate as other
methods, which is why huge amounts of overlap are necessary
especially on regions with repeats.

For lurkers interested in this topic, I found this lecture handout
which covers the differences pretty well:

http://www.ibi.vu.nl/teaching/a4g/materials/lect9.pdf<http://www.ibi.vu.nl/teaching/a4g/materials/lect9.pdf>;


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