There are too many variables to even consider running morphs against wild types. To start with, you will need to run multiple from each lineage in order to reduce the likelihood that you are seeing simple variation across lineages. In the end, you will not come out with the gene of interest. You will end with a number of genes that MAY be involved. As someone using 454 and illumina regularly for my research, I can tell you its not as easy as people might think. Additionally, to do these runs is not exactly cheap. Furthermore, in order to insure accuracy you need sufficient coverage of the genome and that is even more expensive.

Warren
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Dr Warren Booth / Director USARK
North Carolina State University
Department of Entomology

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