This study was funded in part by NSF grant #0211851, #0213764 and by the Initiative for Future Agriculture and Food Systems Grant no. 2001-52100-11292 from the USDA Cooperative State Research, Education, and Extension Service.

Contents:

Our results of the Xu simulations. This is a comparison of five fingerprinting methods. Our results strongly disagree with the results of Xu et al. 2005, and our simulations are much more complete and exhaustive. The simulation software may be downloaded. Reference: William M. Nelson, Jan Dvorak, Ming-Cheng Luo, Joachim Messing, Rod A. Wing and Carol Soderlund (2006). Efficacy of clone fingerprinting methodologies. Genomics 89:160-165. Download

Agarose and HICF with error. Our results show that HICF is much better than Agarose, even when there is error. They also show the benefit of reducing the error in the fingerprints. It is overall cheaper to pay more for less error, as then you need less coverage. Moreover, the precision of your resulting map is better.

Simulation of the MTP software. Our simulations (manuscript in preparation) show that, using HICF fingerprints with a 10x map, gap percentages of 1-3% can be attained with average overlaps of ~30 kb. Adjusting the settings to higher stringency generates higher overlaps and fewer gaps; lower stringency leads to the reverse. With 10x agarose maps, similar gap percentages require higher overlaps, ~50 kb; a 20x map can reduce this to 35 kb. In all cases, addition of a 1x-2x draft sequence set causes a ~10% decrease in overall average overlaps.