SIM.c, a program for local similarities with affine weights, finds k best non-intersecting local alignments and corresponding similarity scores between two sequences or sub-sequences of DNA.
The sim.c program is copyright (c) 1990 by Xiaoqiu Huang and Webb Miller.
The sim.c program, data, and documentation files are archived in sim.shar. The latest table of results (sim.tbl) are available via anonymous ftp from 'ftp.nosc.mil' in directory 'pub/aburto'. The ftp.nosc.mil IP address is: 128.49.192.51 . Please send new results (systems, machines, compilers, compiler options) to 'aburto@marlin.nosc.mil'. I will keep results updated, and periodically post to 'comp.benchmarks'.
Results as of 10 Oct 1993.
NOTES: --- 001 cc +O3 -J 002 cc -O3 -mips2 003 cc -O3 -std1 -non_shared 004 Metaware High C with '-pentium' and 'O4' options, 8 MB 64-bit RAM 005 cc +P +Obb589 +O3 +Om1 -J -Wl,-a,archive $(DEFINES) 006 cc -O3 -migrate -non_shared 007 Apogee AC2.2, venus.nosc.mil, apcc -DUNIX -O5 -cg92 008 cc -O -Q 009 -- 010 cc +P +Obb589 +O3 +Om1 -J -Wl,-a,archive $(DEFINES) 011 cc -O2 012 -- 013 -- 014 -- 015 SC1.0, cc -O2 016 SC2.0.1 06 April 1993, cc -DUNIX -fast -O4 017 -- 018 gcc 2.3.3, gcc -O2 -funroll-loops 019 -- 020 cc 2.3(?), cc -DUNIX -O4. Run under loaded system 021 gcc 2.2.2, gcc -DUNIX -O2 -m486 -fomit-frame-pointer -finline -functions -funroll-all-loops 022 -- 023 -- 024 -- 025 cc -O4 026 cc -DUNIX -O3 027 cc -DUNIX -O4 028 SC1.0, cc -fast -O4 029 cc -DUNIX -O2 030 cc -DUNIX -Bstatic -O4 031 cc -DUNIX -Bstatic -O3 032 SC1.0, cc -fast 033 SC1.1, cc -fast 034 cc -O2 035 cc -DUNIX -O1 036 -- 037 -- 038 cc -DUNIX 039 SC2.0.1 06 Apr 1993, cc -DUNIX -fast -O4 -cg89 040 -- 041 gcc 2.2.2, gcc -DUNIX -m486 -O2 -fomit-frame-pointer 042 gcc 2.2.2, gcc -DUNIX -m486 -O2 -fomit-frame-pointer -fexpensive -optimizations 043 gcc 2.2.2, gcc -DUNIX -O2 -fomit-frame-pointer 044 gcc 2.2.2, gcc -DUNIX -m486 -O2 -fomit-frame-pointer -fexpensive -optimizations -funroll-loops 045 gcc 2.2.2, gcc -DUNIX -m486 -O -fomit-frame-pointer -fexpensive -optimizations -funroll-loops 046 SAS/C 6.3, 68040 code, all optimizations ON, 60 ns RAM. 047 -- 048 gcc 2.2.2, gcc -DUNIX -O2 049 gcc 2.2.2, gcc -DUNIX -O 050 gcc 2.2.2, gcc -DUNIX 051 gcc 1.37.1,gcc -DUNIX -O 052 ---------, gcc -O --- --- REF: 1 Posted to comp.benchmarks, 1993. 2 Al Aburto, aburto@marlin.nosc.mil, 03 Aug 1993 3 Roger Uzun, uzun@crash.cts.com, 19 Aug 1993 4 Timo Suhonen, suhonen@jalka.jyu.fi, 07 Sep 1993 5 Stephen Carpenter, sac@uvo.dec.com, 07 Sep 1993 6 Burkhard Neidecker-Lutz, neideck@neestvx.enet.dec.com, 07 Sep 1993 7 Bo Thide', bt@irfu.se, 20 Sep 1993 8 Al Aburto, aburto@marlin.nosc.mil, 10 Oct 1993 9 Henrik Harmsen, d9hh@dtek.chalmers.se, 10 Oct 1993