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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.

     sortsortsort
  ×   Program Source Code CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
 OCaml 1.5962,9761064  4% 25% 65% 62%
 OCaml #3 0.7830,8401314  52% 29% 60% 78%
 C gcc #2 0.800.54248,720741  15% 20% 40% 76%
 Ada 2005 GNAT #2 0.950.80197,3843220  5% 39% 4% 81%
 C gcc 1.020.71379,2641867  0% 28% 31% 87%
 C++ g++ #4 1.040.68227,9442275  75% 25% 12% 47%
 Go 1.060.94249,6681243  84% 15% 2% 14%
 C++ g++ #2 1.090.81245,0721082  18% 36% 11% 76%
 C gcc #4 1.131.13125,180704  3% 1% 100% 2%
 Fortran Intel 1.161.17246,4881013  0% 0% 100% 1%
 C++ g++ #3 1.161.16125,176810  2% 0% 2% 100%
 Go #2 1.161.16160,672546  97% 2% 2% 2%
 Go #3 1.201.20160,416543  100% 1% 2% 0%
 Rust 1.361.37248,980804  1% 100% 1% 1%
 OCaml #4 1.531.54135,0962064  1% 0% 10% 99%
 Haskell GHC #3 1.591.39126,352999  5% 4% 100% 7%
 Java  #6 1.881.58517,816745  3% 39% 38% 46%
 Scala #8 2.021.54516,736761  3% 92% 5% 35%
 Pascal Free Pascal #2 2.082.08131,492751  0% 0% 100% 1%
 Java  #7 2.358.07270,3761640  40% 7% 23% 75%
 C# Mono 2.392.40172,5401099  3% 66% 0% 34%
 Scala #4 2.402.32411,280501  2% 4% 3% 98%
 Lisp SBCL 2.552.56372,800896  0% 2% 100% 1%
 Java  #4 2.582.48482,760592  75% 2% 24% 4%
 C++ g++ 2.712.71245,432571  0% 1% 1% 100%
 Ada 2005 GNAT 2.792.79123,784885  0% 1% 0% 100%
 Haskell GHC #2 2.842.46618,740919  5% 5% 7% 100%
 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%
 OCaml #2 4.504.51211,504394  0% 0% 0% 100%
 Scala #7 4.952.50711,284949  34% 80% 52% 34%
 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 7.637.64286,444863  84% 2% 17% 1%
 Ruby #2 8.358.36130,032255  0% 100% 1% 0%
 Racket 13.6313.64546,072547  1% 0% 1% 100%
 Clojure 14.156.13488,8281044  50% 47% 81% 56%
 Clojure #4 16.327.29519,016997  58% 69% 36% 62%
 C++ g++ #5 18.6018.61123,428646  1% 1% 1% 100%
 Erlang 18.969.61922,5081302  63% 62% 39% 34%
 Python 3 #3 19.8419.87966,060295  1% 0% 1% 100%
 Erlang HiPE 19.939.98975,1241302  32% 33% 57% 80%
 Dart #3 21.8121.641,759,872551  2% 96% 3% 1%
 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 35.2835.031,885,220555  27% 24% 44% 7%
 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%
Dart Failed443
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 15.807.29655,228812
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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