Wanted: Contig software
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)
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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