We would like to thank our collaborators J. McLaren, PhD from Solvigen and J. Osborne, PhD and M. Lenz, PhD from NC+ Hybrids. The sorghum MF sequence set was generated as part of a Department of Energy matching funds grant (DE-fc36–01ID14212) to Orion Genomics and United States Department of Agriculture IFAFS grant 2001–52100-11331 to RAM and WRM. The sorghum whole-genome shotgun sequences were generated as part of a National Science Foundation Experimental Program to Stimulate Competitive Research grant to BAR. Finally, we would like to thank the Free Software/Open Source community for creating wonderful software and for fielding our questions, especially OpenOffice.org, ImageMagick, BioPerl, and the multitude of Linux groups. ; JAB, MAB, AN, RWC, IFK, PDR, NL, WRM, JAJ, and RAM conceived and designed the experiments. JAB, MAB, AN, RWC, JJ, EF, TR, JF, KB, JM, MS, HH, PDR, and JAJ performed the experiments. JAB, AN, RWC, DR, HH, IFK, PDR, JAJ, and RAM analyzed the data. JAB, BAR, GW, IFK, and PDR contributed reagents/materials/analysis tools. JAB, AN, RWC, IFK, PDR, JAJ, and RAM wrote the paper. ; Methylation filtration makes practical the sequencing of large genomes, such as those found in sorghum, by preferentially capturing functionally relevant sequences.