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

Each chart bar shows how many times slower, one ↓ reverse-complement program was, compared to the fastest program.

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.

    sort sortsort
  ×   Program Source Code CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
1.0Rust #4 0.740.53255,0562015  2% 53% 27% 62%
1.1C gcc #2 0.840.58250,384741  14% 76% 21% 41%
1.3C gcc 1.050.70496,8361867  13% 87% 32% 23%
1.4C++ g++ #4 1.150.75247,0082275  11% 87% 30% 29%
1.7OCaml #3 0.8912,6441314  52% 57% 83% 67%
2.0Fortran Intel 1.021.04246,4601013  1% 0% 1% 100%
2.2Ada 2005 GNAT #2 1.551.15200,6163220  1% 41% 1% 94%
2.2Rust #3 1.171.18254,6521059  0% 100% 0% 2%
2.5C++ g++ #2 1.291.29246,9961082  0% 3% 1% 100%
2.5C gcc #4 1.291.29125,132704  0% 1% 3% 100%
2.5C++ g++ #3 1.321.32124,956810  2% 3% 2% 100%
2.6Java  #3 2.671.36306,1561661  81% 33% 38% 47%
2.7Java  #6 1.681.40519,728745  6% 37% 68% 11%
2.7Scala #8 1.871.41518,472761  1% 39% 3% 91%
2.8Haskell GHC #3 1.541.45125,956999  3% 6% 4% 100%
2.9Rust #2 1.541.55254,660739  1% 100% 0% 1%
3.2OCaml #4 1.661.67127,5802064  0% 1% 1% 100%
3.4Go #3 1.791.79163,280543  1% 3% 2% 99%
3.6Go 2.181.91249,5721243  13% 1% 100% 2%
3.8Go #2 1.981.98163,232546  1% 0% 99% 1%
3.9OCaml 2.0625,4481064  6% 26% 66% 61%
3.9Pascal Free Pascal #2 2.062.06124,428751  0% 1% 0% 100%
4.2Scala #4 2.292.19415,228501  90% 3% 12% 3%
5.3Java  #4 2.872.78481,900592  2% 100% 2% 1%
5.4Lisp SBCL 2.812.82251,104896  0% 1% 0% 100%
5.4Haskell GHC #2 3.152.85618,320919  77% 5% 27% 5%
5.6C# Mono 2.962.97175,5201099  0% 99% 1% 2%
5.8Perl #3 3.043.05374,472284  0% 1% 1% 100%
7.0C++ g++ 3.683.69247,044571  1% 0% 2% 100%
7.7Ada 2005 GNAT 4.034.03125,464885  1% 0% 1% 100%
8.5Racket #2 4.484.48172,5481026  1% 1% 100% 1%
8.6OCaml #2 4.494.50171,972394  0% 16% 84% 0%
8.7Clojure #5 6.784.58562,476727  45% 45% 15% 46%
9.1Clojure 6.154.79418,9401044  15% 49% 55% 13%
12Clojure #4 8.006.31460,640997  12% 11% 99% 7%
12Python 3 #4 6.536.55781,144325  0% 1% 0% 100%
15PHP #2 7.837.85443,496262  0% 100% 0% 0%
15PHP 7.927.95370,544297  0% 13% 88% 0%
16Fortran Intel #2 8.288.30167,656772  0% 0% 0% 100%
17Java  #7 2.908.78270,6881640  36% 27% 35% 18%
17C# Mono #3 9.189.19222,152863  100% 1% 1% 1%
21Ruby #2 11.0311.04129,928255  0% 1% 100% 0%
22Erlang HiPE 21.6611.71762,6001302  80% 40% 26% 40%
26Racket 13.5813.59506,864547  0% 1% 100% 0%
34Dart #3 18.1417.74987,560551  1% 1% 100% 2%
36Ruby JRuby #2 25.5619.061,233,648255  14% 61% 49% 12%
46Dart #2 24.5224.05978,100555  2% 0% 100% 2%
47Python 3 #3 24.6224.65921,520295  0% 0% 1% 100%
48C++ g++ #5 25.1225.13188,568646  0% 0% 1% 100%
70Erlang HiPE #4 45.0536.66689,3681167  77% 22% 9% 17%
112Erlang HiPE #3 61.0558.751,030,104624  4% 0% 1% 99%
155Rust 81.7581.78129,808433  87% 1% 0% 13%
Scala #6 Failed519
Scala #5 Failed329
Scala #7 Failed949
"wrong" (different) algorithm / less comparable programs
2.9Java  1.561.54518,064476
9.1Python 3 #5 4.764.77471,320306
12Clojure #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

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