Wanted: Contig software

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Mon Nov 16 11:26:54 EST 1992


I recommand CAP written by Xiaoqiu Huang.  You can ftp it
from cs.mtu.edu or from ftp.bio.indiana.edu, as /molbio/align/cap.*
GDE uses this program, and SeqApp will as soon as I can get it
to recompile on Macs.

   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 at 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.

-- 
Don Gilbert                                     gilbert at bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405



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