An Assembly Algorithm for DNA Sequence with Repeats

A program for assembling DNA fragments using a new approach has been developed. In the program, a filter and a sequence alignment are used to identify the true overlap between the two fragments. Then the fragments in repeat copies are put into a repeat contig and the others are put into nonrepeat contigs. The repeat contig is resolved into two contigs and then all contigs are merged into one contig. At last the multiple alignment is obtained by the order of fragments in the contig, thereby forming a consensus sequence. The performance tests of the program for eight fragment libraries have demonstrated the feasibility of the program .