CAP -- Contig Assembly Program

CAP -- Contig Assembly Program

CAP (Contig Assembly Program) by Xiaoqiu Huang is a C language program supporting DNA shotgun sequencing, by finding the shortest common superstring of a set of fragments. As to performance, CAP took 4 hours to assemble 1015 fragments of a total of 252,000 characters on a Sun SPARCstation SLC. Certain parameters will need to be tweaked to make it accommodate non-DNA data. It is available by anonymous ftp from cs.mtu.edu in the pub/huang directory. MAP (Multiple Alignment Program) also by Xiaoqiu Huang is a C language program computes a multiple global alignment of sequences using an iterative pairwise method. It is also available by anonymous ftp from cs.mtu.edu in the pub/huang directory.
  • Download Files (local site)
  • Author's homepage with original sources

    Problem Links

  • Longest Common Substring (8)
  • Shortest Common Superstring (8)

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    This page last modified on Oct 16, 1996.