reverse-complement benchmark ≈240MB N=25,000,000

Each chart bar shows how many times more Memory, one ↓ reverse-complement program used, compared to the program that used least Memory.

These are not the only programs that could be written. These are not the only compilers and interpreters. These are not the only programming languages.

Column × shows how many times more each program used compared to the benchmark program that used least.

    sortsort sort
  ×   Program Source Code CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
1.0OCaml #3 0.8912,6441314  52% 57% 83% 67%
2.0OCaml 2.0625,4481064  6% 26% 66% 61%
9.8Pascal Free Pascal #2 2.062.06124,428751  0% 1% 0% 100%
9.9C++ g++ #3 1.321.32124,956810  2% 3% 2% 100%
9.9C gcc #4 1.291.29125,132704  0% 1% 3% 100%
10Ada 2005 GNAT 4.034.03125,464885  1% 0% 1% 100%
10Haskell GHC #3 1.541.45125,956999  3% 6% 4% 100%
10OCaml #4 1.661.67127,5802064  0% 1% 1% 100%
10Rust 81.7581.78129,808433  87% 1% 0% 13%
10Ruby #2 11.0311.04129,928255  0% 1% 100% 0%
13Go #3 1.721.72164,092543  1% 4% 100% 1%
13Go #2 2.012.01164,092546  0% 1% 1% 100%
13Fortran Intel #2 8.288.30167,656772  0% 0% 0% 100%
14OCaml #2 4.494.50171,972394  0% 16% 84% 0%
14Racket #2 4.484.48172,5481026  1% 1% 100% 1%
14C# Mono 2.962.97175,5201099  0% 99% 1% 2%
15C++ g++ #5 25.1225.13188,568646  0% 0% 1% 100%
16Ada 2005 GNAT #2 1.551.15200,6163220  1% 41% 1% 94%
17Lisp SBCL 3.203.21216,240896  1% 1% 100% 0%
18C# Mono #3 9.189.19222,152863  100% 1% 1% 1%
19Fortran Intel 1.021.04246,4601013  1% 0% 1% 100%
20C++ g++ #2 1.291.29246,9961082  0% 3% 1% 100%
20C++ g++ #4 1.150.75247,0082275  11% 87% 30% 29%
20C++ g++ 3.683.69247,044571  1% 0% 2% 100%
20Go 2.161.89249,5601243  2% 3% 99% 13%
20C gcc #2 0.840.58250,384741  14% 76% 21% 41%
20Rust #3 1.171.18254,6521059  0% 100% 0% 2%
20Rust #2 1.541.55254,660739  1% 100% 0% 1%
20Rust #4 0.740.53255,0562015  2% 53% 27% 62%
21Java  #7 2.908.78270,6881640  36% 27% 35% 18%
24Java  #3 2.671.36306,1561661  81% 33% 38% 47%
29PHP 7.927.95370,544297  0% 13% 88% 0%
30Perl #3 3.043.05374,472284  0% 1% 1% 100%
33Scala #4 2.292.19415,228501  90% 3% 12% 3%
33Clojure 6.154.79418,9401044  15% 49% 55% 13%
35PHP #2 7.837.85443,496262  0% 100% 0% 0%
36Clojure #4 8.006.31460,640997  12% 11% 99% 7%
38Java  #4 2.872.78481,900592  2% 100% 2% 1%
39C gcc 1.050.70496,8361867  13% 87% 32% 23%
40Racket 13.5813.59506,864547  0% 1% 100% 0%
41Scala #8 1.871.41518,472761  1% 39% 3% 91%
41Java  #6 1.681.40519,728745  6% 37% 68% 11%
44Clojure #5 6.784.58562,476727  45% 45% 15% 46%
49Haskell GHC #2 3.152.85618,320919  77% 5% 27% 5%
53Erlang HiPE #4 44.4936.04669,0561167  20% 11% 27% 67%
62Python 3 #4 6.536.55781,144325  0% 1% 0% 100%
67Erlang HiPE 21.0811.00844,9201302  43% 50% 51% 50%
69Erlang HiPE #3 58.6556.93867,712624  4% 93% 0% 7%
73Python 3 #3 24.6224.65921,520295  0% 0% 1% 100%
77Dart #3 18.4817.88977,064551  73% 4% 29% 3%
77Dart #2 26.0425.44978,472555  54% 2% 46% 2%
98Ruby JRuby #2 25.5619.061,233,648255  14% 61% 49% 12%
Scala #6 Failed519
Scala #5 Failed329
Scala #7 Failed949
"wrong" (different) algorithm / less comparable programs
37Python 3 #5 4.764.77471,320306
41Java  1.561.54518,064476
44Clojure #3 7.586.40562,384812
missing benchmark programs
F# Mono No program

 reverse-complement benchmark : Read DNA sequences - write their reverse-complement

You can write your own program for this task and contribute to the benchmarks game by following these general instructions.

More specifically:

diff program output for this 10KB input file (generated with the fasta program N = 1000) with this output file to check your program is correct before contributing.

We are trying to show the performance of various programming language implementations - so we ask that contributed programs not only give the correct result, but also use the same algorithm to calculate that result.

We use the FASTA file generated by the fasta benchmark as input for this benchmark. Note: the file may include both lowercase and uppercase codes.

Each program should

We use these code complements:

code  meaning   complement
A    A                   T
C    C                   G
G    G                   C
T/U  T                   A
M    A or C              K
R    A or G              Y
W    A or T              W
S    C or G              S
Y    C or T              R
K    G or T              M
V    A or C or G         B
H    A or C or T         D
D    A or G or T         H
B    C or G or T         V
N    G or A or T or C    N

"by knowing the sequence of bases of one strand of DNA we immediately know the sequence of the DNA strand which will bind to it, this strand is called the reverse complement"
DNA: Structure and Function

Revised BSD license

  Home   Conclusions   License   Play