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 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 2.1512,8801314  0% 0% 1% 100%
2.0OCaml 3.1225,7041064  0% 0% 0% 100%
9.7C++ g++ #3 1.331.34124,968810  0% 1% 0% 99%
9.7C gcc #4 1.331.33125,096704  0% 2% 2% 100%
9.8Haskell GHC #3 1.221.22125,892999  0% 2% 2% 100%
9.9C CINT #2 77.3377.34127,432727  0% 0% 0% 100%
10OCaml #4 1.661.66127,5842064  0% 1% 1% 100%
10Ruby #2 10.6310.64127,856255  0% 1% 0% 100%
10Ada 2005 GNAT 4.154.16128,244885  0% 1% 1% 100%
10Pascal Free Pascal #2 2.162.18128,584751  1% 1% 0% 100%
12Go #3 1.821.82159,884543  0% 0% 1% 100%
12Go #2 2.512.52160,132546  1% 2% 1% 100%
13C# Mono 2.832.83171,2681099  1% 1% 1% 100%
13Racket #2 4.504.51171,8001026  1% 1% 1% 100%
13OCaml #2 4.504.51171,972394  0% 0% 0% 100%
14C++ g++ #5 27.2827.30174,388646  1% 1% 1% 100%
14Fortran Intel #2 8.518.53176,104772  0% 1% 1% 100%
14JavaScript V8 25.5925.61182,832390  0% 1% 1% 100%
14JavaScript V8 #3 12.2412.26183,000498  0% 0% 1% 100%
15Ada 2005 GNAT #2 1.621.64197,1203220  0% 1% 1% 99%
17Lisp SBCL 4.304.30224,968896  0% 1% 1% 100%
19JavaScript V8 #4 9.179.18240,648787  0% 0% 1% 100%
19C++ g++ #2 1.261.26244,8721082  0% 0% 1% 100%
19C++ g++ 3.943.95245,220571  0% 1% 1% 100%
19C++ g++ #4 1.061.07245,4082275  0% 0% 2% 99%
19Fortran Intel 1.031.04246,4641013  0% 0% 3% 100%
19C gcc #2 0.820.83248,640741  0% 0% 2% 100%
19Rust 1.321.33248,884804  2% 1% 1% 100%
19Go 2.182.18249,2001243  0% 0% 0% 100%
20C# Mono #3 9.239.24253,776863  0% 0% 1% 100%
21Java  #7 2.388.24265,3241640  37% 48% 1% 95%
23Java  #3 2.842.85295,5761661  0% 2% 2% 100%
25JavaScript V8 #2 23.3823.41324,524456  0% 1% 1% 100%
29PHP 7.967.98369,064297  0% 1% 1% 100%
29Smalltalk VisualWorks 27.3927.42373,712754  0% 1% 1% 100%
29Perl #3 3.023.03374,264284  1% 0% 0% 100%
32Clojure 6.486.49406,9521044  0% 1% 1% 100%
32Scala #4 2.462.47407,288501  0% 1% 1% 100%
34PHP #2 7.867.88443,500262  0% 0% 0% 100%
35Clojure #4 7.977.98446,216997  1% 0% 1% 100%
35Scala #8 2.122.14453,280761  1% 0% 1% 100%
37Java  #4 3.113.12476,804592  1% 1% 0% 100%
39C gcc 1.071.08496,9241867  0% 1% 2% 100%
39Racket 13.5513.57506,856547  0% 1% 1% 100%
40Java  #6 1.961.97513,448745  1% 2% 0% 100%
44Erlang HiPE 21.2421.26563,3481302  0% 0% 0% 100%
45Haskell GHC #2 2.602.60580,368919  0% 3% 0% 100%
49Erlang HiPE #4 34.5734.60625,9481167  0% 1% 1% 100%
56Lua 22.4922.51724,576555  0% 0% 0% 100%
61Python 3 #4 6.546.56781,140325  1% 0% 1% 100%
62Scala #7 4.804.82797,196949  0% 1% 1% 100%
67Erlang HiPE #3 50.9350.99861,592624  0% 0% 0% 100%
71Python 3 #3 24.5924.62911,484295  0% 1% 0% 100%
87Dart #3 22.7122.741,122,672551  0% 1% 1% 100%
88Dart #2 34.0534.101,136,408555  0% 0% 1% 100%
92Ruby JRuby #2 25.2725.301,189,288255  0% 1% 0% 100%
Dart Failed443
Lua #3 Failed593
Scala #6 Failed519
Scala #5 Failed329
"wrong" (different) algorithm / less comparable programs
37Python 3 #5 4.724.73480,296306
40Java  1.871.88512,512476
41JavaScript V8 #5 52.3252.38522,820407
43Clojure #3 7.707.71556,088812
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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