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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 0.820.83248,640741  0% 0% 2% 100%
1.3Fortran Intel 1.031.04246,4641013  0% 0% 3% 100%
1.3C++ g++ #4 1.061.07245,4082275  0% 0% 2% 99%
1.3C gcc 1.071.08496,9241867  0% 1% 2% 100%
1.5Haskell GHC #3 1.221.22125,892999  0% 2% 2% 100%
1.5C++ g++ #2 1.261.26244,8721082  0% 0% 1% 100%
1.6Rust 1.321.33248,884804  2% 1% 1% 100%
1.6C gcc #4 1.331.33125,096704  0% 2% 2% 100%
1.6C++ g++ #3 1.331.34124,968810  0% 1% 0% 99%
2.0Ada 2005 GNAT #2 1.621.64197,1203220  0% 1% 1% 99%
2.0OCaml #4 1.661.66127,5842064  0% 1% 1% 100%
2.2Go #3 1.821.82159,884543  0% 0% 1% 100%
2.4Java  #6 1.961.97513,448745  1% 2% 0% 100%
2.6Scala #8 2.122.14453,280761  1% 0% 1% 100%
2.6OCaml #3 2.1512,8801314  0% 0% 1% 100%
2.6Pascal Free Pascal #2 2.162.18128,584751  1% 1% 0% 100%
2.6Go 2.182.18249,2001243  0% 0% 0% 100%
3.0Scala #4 2.462.47407,288501  0% 1% 1% 100%
3.0Go #2 2.512.52160,132546  1% 2% 1% 100%
3.1Haskell GHC #2 2.602.60580,368919  0% 3% 0% 100%
3.4C# Mono 2.832.83171,2681099  1% 1% 1% 100%
3.4Java  #3 2.842.85295,5761661  0% 2% 2% 100%
3.7Perl #3 3.023.03374,264284  1% 0% 0% 100%
3.8Java  #4 3.113.12476,804592  1% 1% 0% 100%
3.8OCaml 3.1225,7041064  0% 0% 0% 100%
4.8C++ g++ 3.943.95245,220571  0% 1% 1% 100%
5.0Ada 2005 GNAT 4.154.16128,244885  0% 1% 1% 100%
5.2Lisp SBCL 4.304.30224,968896  0% 1% 1% 100%
5.4OCaml #2 4.504.51171,972394  0% 0% 0% 100%
5.4Racket #2 4.504.51171,8001026  1% 1% 1% 100%
5.8Scala #7 4.804.82797,196949  0% 1% 1% 100%
7.9Python 3 #4 6.546.56781,140325  1% 0% 1% 100%
9.5PHP #2 7.867.88443,500262  0% 0% 0% 100%
9.6PHP 7.967.98369,064297  0% 1% 1% 100%
10Java  #7 2.388.24265,3241640  37% 48% 1% 95%
10Fortran Intel #2 8.518.53176,104772  0% 1% 1% 100%
11JavaScript V8 #4 9.179.18240,648787  0% 0% 1% 100%
11C# Mono #3 9.239.24253,776863  0% 0% 1% 100%
13Ruby #2 10.6310.64127,856255  0% 1% 0% 100%
15JavaScript V8 #3 12.2412.26183,000498  0% 0% 1% 100%
16Racket 13.5513.57506,856547  0% 1% 1% 100%
18Clojure 15.1015.12494,8281044  0% 1% 0% 100%
20Clojure #4 16.9016.92533,616997  0% 1% 1% 100%
26Erlang HiPE 21.2421.26563,3481302  0% 0% 0% 100%
27Lua 22.4922.51724,576555  0% 0% 0% 100%
27Dart #3 22.7122.741,122,672551  0% 1% 1% 100%
28JavaScript V8 #2 23.3823.41324,524456  0% 1% 1% 100%
30Python 3 #3 24.5924.62911,484295  0% 1% 0% 100%
31Ruby JRuby #2 25.2725.301,189,288255  0% 1% 0% 100%
31JavaScript V8 25.5925.61182,832390  0% 1% 1% 100%
33C++ g++ #5 27.2827.30174,388646  1% 1% 1% 100%
33Smalltalk VisualWorks 27.3927.42373,712754  0% 1% 1% 100%
41Dart #2 34.0534.101,136,408555  0% 0% 1% 100%
42Erlang HiPE #4 34.5734.60625,9481167  0% 1% 1% 100%
62Erlang HiPE #3 50.9350.99861,592624  0% 0% 0% 100%
93C CINT #2 77.3377.34127,432727  0% 0% 0% 100%
Dart Failed443
Lua #3 Failed593
Scala #6 Failed519
Scala #5 Failed329
"wrong" (different) algorithm / less comparable programs
2.3Java  1.871.88512,512476
5.7Python 3 #5 4.724.73480,296306
20Clojure #3 16.4416.46637,516812
63JavaScript V8 #5 52.3252.38522,820407
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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