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 0.7830,8401314  52% 29% 60% 78%
2.0OCaml 1.5962,9761064  4% 25% 65% 62%
4.1C++ g++ #3 1.241.24125,160810  1% 1% 3% 100%
4.1C gcc #4 1.141.14125,212704  0% 3% 100% 0%
4.1Pascal Free Pascal #2 2.022.02125,648751  1% 0% 100% 2%
4.1Ada 2005 GNAT 5.705.71125,744885  1% 96% 0% 4%
4.1Haskell GHC #3 1.551.38126,340999  99% 4% 4% 4%
4.2Ruby #2 8.358.36130,032255  0% 100% 1% 0%
4.4OCaml #4 1.531.54135,0962064  1% 0% 10% 99%
5.2Go #3 1.181.18160,140543  2% 1% 1% 99%
5.2Go #2 1.101.10160,660546  2% 1% 99% 0%
5.6Racket #2 4.364.36171,3081026  0% 1% 100% 1%
5.7Fortran Intel #2 6.476.48174,276772  0% 0% 0% 100%
5.8C# Mono 2.792.79178,7001099  85% 1% 16% 1%
6.0C++ g++ #5 19.3719.38185,728646  0% 1% 100% 1%
6.4Ada 2005 GNAT #2 0.980.83198,9083220  31% 80% 11% 4%
6.9OCaml #2 4.504.51211,504394  0% 0% 0% 100%
8.0Fortran Intel 1.161.17246,4881013  0% 0% 100% 1%
8.0C++ g++ #2 1.061.06247,1561082  0% 2% 4% 100%
8.0C++ g++ 2.702.71247,208571  3% 1% 100% 1%
8.0C++ g++ #4 1.020.65247,5082275  17% 64% 34% 48%
8.1Go 0.930.77250,5641243  10% 69% 11% 35%
8.1C gcc #2 0.770.51250,784741  21% 18% 74% 43%
8.8Java  #7 2.358.07270,3761640  40% 7% 23% 75%
9.6C# Mono #3 8.328.33295,584863  97% 1% 3% 0%
9.8Java  #3 2.971.47300,7121661  47% 37% 78% 43%
12PHP 6.596.61369,940297  0% 0% 0% 100%
12Perl #3 2.902.90374,704284  0% 0% 0% 100%
13Lisp SBCL 2.412.42396,200896  0% 0% 0% 100%
13Clojure 4.773.42402,8561044  32% 9% 83% 16%
13Scala #4 2.402.32411,280501  2% 4% 3% 98%
14PHP #2 6.406.41444,376262  0% 0% 0% 100%
14C gcc 0.970.61445,9441867  25% 3% 98% 37%
14Clojure #4 5.874.38446,840997  98% 14% 13% 12%
16Java  #4 2.582.48482,760592  75% 2% 24% 4%
16Hack 22.2722.31484,040294  1% 100% 0% 0%
17Scala #8 2.021.54516,736761  3% 92% 5% 35%
17Java  #6 1.881.58517,816745  3% 39% 38% 46%
18Racket 13.6313.64546,072547  1% 0% 1% 100%
19Clojure #5 4.382.86571,340727  44% 30% 64% 19%
20Haskell GHC #2 2.842.44618,532919  6% 6% 100% 7%
21Hack #2 22.1722.21645,024261  1% 0% 0% 100%
21Erlang #4 46.5936.70662,4201167  94% 11% 12% 10%
23Scala #7 4.952.50711,284949  34% 80% 52% 34%
25Erlang HiPE #4 42.5534.03776,8601167  79% 26% 12% 8%
30Erlang 18.969.61922,5081302  63% 62% 39% 34%
31Python 3 #3 19.8419.87966,060295  1% 0% 1% 100%
32Erlang HiPE 19.939.98975,1241302  32% 33% 57% 80%
33Python 3 #4 5.925.941,008,592325  1% 1% 1% 100%
37Erlang #3 69.7667.791,150,856624  52% 1% 0% 50%
40Ruby JRuby #2 26.4619.661,243,664255  12% 49% 61% 15%
50Erlang HiPE #3 57.2054.451,537,668624  1% 99% 9% 1%
58Dart #3 21.5221.021,793,164551  1% 1% 100% 3%
59Dart #2 34.2733.681,821,968555  1% 2% 2% 100%
Scala #6 Failed519
Scala #5 Failed329
"wrong" (different) algorithm / less comparable programs
16Python 3 #5 4.094.10482,816306
17Java  1.791.76516,244476
18Clojure #3 5.524.37567,820812
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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