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 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 0.800.54248,720741  15% 20% 40% 76%
1.3C++ g++ #4 1.040.68227,9442275  75% 25% 12% 47%
1.3C gcc 1.020.71379,2641867  0% 28% 31% 87%
1.4OCaml #3 0.7830,8401314  52% 29% 60% 78%
1.5Ada 2005 GNAT #2 0.950.80197,3843220  5% 39% 4% 81%
1.5C++ g++ #2 1.090.81245,0721082  18% 36% 11% 76%
1.7Go 1.060.94249,6681243  84% 15% 2% 14%
2.1C gcc #4 1.131.13125,180704  3% 1% 100% 2%
2.1C++ g++ #3 1.161.16125,176810  2% 0% 2% 100%
2.1Go #2 1.161.16160,672546  97% 2% 2% 2%
2.1Fortran Intel 1.161.17246,4881013  0% 0% 100% 1%
2.2Go #3 1.201.20160,416543  100% 1% 2% 0%
2.5Rust 1.361.37248,980804  1% 100% 1% 1%
2.5Haskell GHC #3 1.551.38126,340999  99% 4% 4% 4%
2.7Java  #3 2.971.47300,7121661  47% 37% 78% 43%
2.8OCaml #4 1.531.54135,0962064  1% 0% 10% 99%
2.8Scala #8 2.021.54516,736761  3% 92% 5% 35%
2.9Java  #6 1.881.58517,816745  3% 39% 38% 46%
2.9OCaml 1.5962,9761064  4% 25% 65% 62%
3.8Pascal Free Pascal #2 2.082.08131,492751  0% 0% 100% 1%
4.3Scala #4 2.402.32411,280501  2% 4% 3% 98%
4.4C# Mono 2.392.40172,5401099  3% 66% 0% 34%
4.5Haskell GHC #2 2.842.44618,532919  6% 6% 100% 7%
4.6Java  #4 2.582.48482,760592  75% 2% 24% 4%
4.6Scala #7 4.952.50711,284949  34% 80% 52% 34%
4.7Lisp SBCL 2.552.56372,800896  0% 2% 100% 1%
5.0C++ g++ 2.712.71245,432571  0% 1% 1% 100%
5.1Ada 2005 GNAT 2.792.79123,784885  0% 1% 0% 100%
5.3Perl #3 2.902.90374,704284  0% 0% 0% 100%
6.3Clojure 4.773.42402,8561044  32% 9% 83% 16%
8.0Racket #2 4.364.36171,3081026  0% 1% 100% 1%
8.1Clojure #4 5.874.38446,840997  98% 14% 13% 12%
8.3OCaml #2 4.504.51211,504394  0% 0% 0% 100%
11Python 3 #4 5.925.941,008,592325  1% 1% 1% 100%
12PHP #2 6.406.41444,376262  0% 0% 0% 100%
12Fortran Intel #2 6.476.48174,276772  0% 0% 0% 100%
12PHP 6.596.61369,940297  0% 0% 0% 100%
14C# Mono #3 7.637.64286,444863  84% 2% 17% 1%
15Java  #7 2.358.07270,3761640  40% 7% 23% 75%
15Ruby #2 8.358.36130,032255  0% 100% 1% 0%
18Erlang 18.969.61922,5081302  63% 62% 39% 34%
18Erlang HiPE 19.939.98975,1241302  32% 33% 57% 80%
25Racket 13.6313.64546,072547  1% 0% 1% 100%
34C++ g++ #5 18.6018.61123,428646  1% 1% 1% 100%
36Ruby JRuby #2 26.4619.661,243,664255  12% 49% 61% 15%
37Python 3 #3 19.8419.87966,060295  1% 0% 1% 100%
39Dart #3 21.6021.431,792,652551  1% 64% 33% 5%
41Hack #2 22.1722.21645,024261  1% 0% 0% 100%
41Hack 22.2722.31484,040294  1% 100% 0% 0%
61Dart #2 33.5833.321,903,496555  63% 31% 4% 4%
63Erlang HiPE #4 42.5534.03776,8601167  79% 26% 12% 8%
67Erlang #4 46.5936.70662,4201167  94% 11% 12% 10%
100Erlang HiPE #3 57.2054.451,537,668624  1% 99% 9% 1%
125Erlang #3 69.7667.791,150,856624  52% 1% 0% 50%
Dart Failed443
Scala #6 Failed519
Scala #5 Failed329
"wrong" (different) algorithm / less comparable programs
3.2Java  1.791.76516,244476
7.5Python 3 #5 4.094.10482,816306
8.0Clojure #3 5.524.37567,820812
missing benchmark programs
F# Mono 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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