CONTIG ASSEMBLY PROGRAM (CAP) copyright (c) 1992 Xiaoqiu Huang The distribution of the program is granted provided no charge is made and the copyright notice is included. Proper attribution of the author as the source of the software would be appreciated: "A Contig Assembly Program Based on Sensitive Detection of Fragment Overlaps" (Genomics, 1992, in press) Xiaoqiu Huang Department of Computer Science Michigan Technological University Houghton, MI 49931 E-mail: huang@cs.mtu.edu The CAP program uses a dynamic programming algorithm to compute the maximal-scoring overlapping alignment between two fragments. Fragments in random orientations are assembled into contigs by a greedy approach in order of the overlap scores. CAP is efficient in computer memory: a large number of arbitrarily long fragments can be assembled. The time requirement is acceptable; for example, CAP took 4 hours to assemble 1015 fragments of a total of 252 kb nucleotides on a Sun SPARCstation SLC. The program is written in C and runs on Sun workstations.