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.

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

  Home   Conclusions   License   Play