The DOS version of the SIM program is now available
from both University of Houston and EMBL file servers.
To obtain DOS version from the Houston Server, send the command
send dos sim-all.uue
gene-server at bchs.uh.edu (internet)
gene-server%bchs.uh.edu at CUNYVM (BITNET)
To obtain DOS or VAX version from EMBL, send the commands
GET DOS_SOFTWARE:SIM.UUE or GET VAX_SOFTWARE:SIM.UUE
NETSERV at EMBL.BITNET
(Note that the Unix version is also available from both servers.)
SIM finds k best non-intersecting local alignments between two
sequences or within one sequence. Using dynamic programming
techniques, SIM is guaranteed to find optimal alignments.
The alignments are reported in order of similarity score.
The main strength of SIM is its low space requirement.
SIM works for nucleic acid and protein sequences.
The SIM program is written in C and is portable to many machines.
For the description of the algorithm, please see the paper
"A Time-Efficient, Linear-Space Local Similarity Algorithm"
Xiaoqiu Huang and Webb Miller
(Advances in Applied Mathematics, in press)
An early version of this program is presented in the paper
"A Space-Efficient Algorithm for Local Similarities"
Xiaoqiu Huang, Ross C. Hardison and Webb Miller
(Computer Applications in the Biosciences, 6(4): 373-381)
Department of Computer Science
Michigan Technological University
Houghton, MI 49931
E-mail: huang at cs.mtu.edu