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
1.0C gcc #2 0.670.67250,856741  3% 0% 2% 100%
1.1C gcc 0.740.74403,4681867  1% 0% 4% 100%
1.2Go 0.820.82250,8441243  0% 0% 2% 100%
1.3C++ g++ #4 0.870.87245,7242275  3% 1% 0% 100%
1.5Ada 2005 GNAT #2 0.970.98198,8883220  0% 0% 2% 99%
1.6C++ g++ #2 1.051.06247,0561082  0% 1% 4% 100%
1.6Go #2 1.101.10160,412546  0% 4% 1% 99%
1.7C gcc #4 1.141.14125,212704  0% 0% 2% 100%
1.7Fortran Intel 1.161.17153,5601013  3% 1% 2% 100%
1.7Go #3 1.171.17160,292543  1% 1% 0% 100%
1.8Haskell GHC #3 1.191.19126,148999  0% 1% 0% 99%
1.8C++ g++ #3 1.231.23125,160810  2% 0% 1% 100%
2.3OCaml #3 1.5431,3161314  1% 1% 2% 100%
2.5OCaml #4 1.521.66135,0962064  0% 0% 2% 100%
2.8Java  #6 1.861.87517,532745  0% 1% 1% 100%
2.9Scala #8 1.951.96516,716761  2% 0% 1% 100%
3.0Pascal Free Pascal #2 2.022.02123,976751  3% 0% 2% 100%
3.2Haskell GHC #2 2.172.18618,908919  1% 0% 2% 100%
3.4OCaml 2.3262,9841064  0% 0% 1% 100%
3.6Scala #4 2.402.40410,720501  1% 0% 1% 100%
3.6Lisp SBCL 2.412.41396,200896  0% 1% 1% 100%
3.8Java  #4 2.562.57481,176592  3% 1% 3% 100%
4.0C++ g++ 2.702.71247,168571  0% 1% 0% 100%
4.0Java  #3 2.702.71300,4241661  0% 0% 1% 100%
4.1C# Mono 2.772.78180,7201099  1% 1% 1% 100%
4.3Perl #3 2.902.91374,548284  0% 0% 0% 100%
5.8Scala #7 3.863.87801,600949  0% 1% 1% 100%
6.2Clojure #5 4.104.13561,016727  1% 1% 0% 100%
6.5Racket #2 4.364.36171,3161026  0% 0% 1% 100%
6.5Clojure 4.384.39410,7321044  0% 1% 1% 100%
6.7OCaml #2 4.484.49211,500394  0% 0% 0% 100%
8.3Clojure #4 5.545.55447,524997  1% 1% 1% 100%
8.5Ada 2005 GNAT 5.725.72125,448885  1% 0% 1% 100%
8.9Python 3 #4 5.986.001,008,592325  0% 1% 1% 100%
9.6PHP #2 6.416.42444,380262  0% 0% 0% 100%
9.7Fortran Intel #2 6.486.49165,828772  0% 0% 0% 100%
9.8PHP 6.566.58369,944297  0% 0% 0% 100%
11JavaScript V8 #4 7.367.37398,528787  0% 1% 1% 100%
12C# Mono #3 7.767.77290,544863  0% 1% 1% 100%
12Ruby #2 8.358.36130,036255  0% 1% 0% 100%
14Java  #7 2.169.23270,5361640  48% 24% 1% 96%
20Racket 13.6613.68546,088547  1% 0% 1% 100%
22JavaScript V8 #3 14.5214.53387,068498  0% 1% 0% 100%
27Lua 18.3418.37796,612555  0% 0% 0% 100%
29Erlang HiPE 19.2019.23632,6161302  0% 0% 0% 100%
29C++ g++ #5 19.3719.38142,176646  1% 0% 1% 100%
30Python 3 #3 19.9419.97983,752295  1% 1% 1% 100%
32Dart #3 21.6521.671,746,100551  1% 1% 0% 100%
33Hack 22.2522.29518,116294  0% 0% 1% 100%
34Hack #2 22.8622.89582,200261  1% 0% 1% 100%
37JavaScript V8 #2 24.5424.58647,952456  0% 1% 0% 100%
38Ruby JRuby #2 25.5325.561,157,700255  1% 1% 1% 100%
46Smalltalk VisualWorks 31.1031.13331,836754  0% 0% 0% 100%
51Erlang HiPE #4 34.1934.22596,8161167  0% 0% 0% 100%
52Dart #2 34.9535.001,753,532555  1% 2% 0% 100%
53JavaScript V8 35.3935.43378,052390  1% 5% 2% 100%
73Erlang HiPE #3 48.6648.741,307,344624  0% 0% 0% 100%
Lua #3 Failed593
Scala #6 Failed519
Scala #5 Failed329
"wrong" (different) algorithm / less comparable programs
2.7Java  1.791.79516,224476
6.1Python 3 #5 4.074.08488,100306
8.1Clojure #3 5.425.43562,780812
68JavaScript V8 #5 45.4145.47934,460407
missing benchmark programs
F# Mono No program
Rust No program

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

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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