Optical mapping is a method by which large-scale, efficient restriction digests can be utilized as an alternative to sequence assembly. In traditional sequence assembly, a genetic target is fragmented, amplified, and sequenced. Software algorithms then find stretches of similar sequence in sets of sequencing reads and align these sequences to each other, building consensus sequences that are intended to represent the biological genetic sequence. In optical mapping, the genetic target is subjected to a restriction digest and then imaged to appraise the length of the fragments. A key difference from other restriction techniques is that the order of the restriction fragments with respect to each other is known. A software algorithm then aligns the digested fragments of DNA to each other to generate a restriction map for the entire genetic target. We propose to design a map-assisted assembler in which the data from optical mapping are integrated into our re-engineered Phrap assembler. The optical map data will be used in the assembler to 1) verify the correctness of the assembly, 2) align assembled contigs into supertigs, and 3) prevent misassembly. ? ?
