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<html> <body> Hi all. We're having trouble with our positional cloning project, and we hoping for some input on the following two questions: 1) Are others noticing a great deal of misassembly to the genome still?  It seems that every new release of the assembly, our markers jump all over.  For example, on Zv5 we had two markers 500 kb apart, which went to 12 megabases apart on Zv6.  We kept walking, and got down to 4 MB, but then Zv7 pushed those 7 MB apart.  Furthermore, Zv7 has three of our favorite markers in order A-B-C on the genome, but our data has them A-C-B.  (as an aside, we are looking at another gene, and have found it (all 800 bp) with the identical DNA sequence on two different chromosomes on Zv7.  Even if these are redundant copies, how likely is it that they will match at 800 of 800 bp, or is this a sign of further misassembly?) 2) This is the crossing strategy we used.  Are there any glaring errors in this that could be causing us problems or are we o.k.? <x-tab>        </x-tab>a) A female AB carrying the mutation was crossed to a male WIK.  Embryos were collected for positional cloning from this mapcross.  However, we ran out of embryo DNA and the mapcross line got old and stopped laying well.  So, <x-tab>        </x-tab>b) A male from the above mapcross was backcrossed to a female WIK.  We continue to collect embryos from this mapcross backcross. I wasn't sure if I read somewhere if it makes a great difference if the crosses to the mapping line are against females or males. Thanks for any advice, comments. Tom <x-sigsep></x-sigsep> Thomas Bartman, M.D., Ph.D. Divisions of Neonatology, Pulmonary Biology, and Developmental Biology Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7009 Cincinnati, OH  45229-3039 Office: 513-636-9902</body> </html>

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