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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 0.8912,6441314  52% 57% 83% 67%
2.0OCaml 2.0625,4481064  6% 26% 66% 61%
9.7Pascal Free Pascal #2 2.172.17122,544751  0% 0% 0% 100%
9.9C++ g++ #3 1.321.32124,956810  2% 3% 2% 100%
9.9C gcc #4 1.291.29125,132704  0% 1% 3% 100%
10Haskell GHC #3 1.541.45125,956999  3% 6% 4% 100%
10OCaml #4 1.661.67127,5802064  0% 1% 1% 100%
10Ruby #2 10.6110.62127,848255  0% 0% 100% 1%
10Ada 2005 GNAT 4.144.15130,092885  0% 1% 100% 1%
13Go #3 1.821.82159,880543  2% 0% 0% 100%
13Go #2 2.522.52160,120546  0% 100% 0% 0%
13Fortran Intel #2 8.288.30167,656772  0% 0% 0% 100%
14C# Mono 2.822.82171,2721099  1% 74% 2% 26%
14OCaml #2 4.494.50171,972394  0% 16% 84% 0%
14Racket #2 4.484.48172,5481026  1% 1% 100% 1%
15C++ g++ #5 25.1225.13188,568646  0% 0% 1% 100%
16Ada 2005 GNAT #2 1.641.24197,1243220  42% 1% 26% 64%
17Lisp SBCL 4.304.31219,636896  0% 0% 0% 100%
19Fortran Intel 1.021.04246,4601013  1% 0% 1% 100%
20C++ g++ #2 1.291.29246,9961082  0% 3% 1% 100%
20C++ g++ #4 1.150.75247,0082275  11% 87% 30% 29%
20C++ g++ 3.683.69247,044571  1% 0% 2% 100%
20Rust 1.331.33248,880804  0% 0% 100% 0%
20Go 2.281.93249,1641243  3% 16% 6% 98%
20C gcc #2 0.840.58250,384741  14% 76% 21% 41%
20C# Mono #3 9.209.21255,164863  0% 100% 0% 0%
21Java  #7 2.707.31264,9121640  28% 28% 18% 45%
23Java  #3 3.161.63296,1361661  77% 24% 39% 58%
29PHP 7.927.95370,544297  0% 13% 88% 0%
30Perl #3 3.043.05374,472284  0% 1% 1% 100%
32Clojure 6.435.09405,1641044  11% 6% 98% 12%
32Scala #4 2.482.41406,492501  2% 2% 98% 5%
35PHP #2 7.837.85443,496262  0% 100% 0% 0%
35Clojure #4 8.026.50446,884997  49% 8% 11% 58%
38Java  #4 3.143.04478,080592  3% 98% 2% 3%
39C gcc 1.050.70496,8361867  13% 87% 32% 23%
40Racket 13.5813.59506,864547  0% 1% 100% 0%
41Scala #8 2.201.69512,996761  92% 6% 33% 2%
41Java  #6 2.011.74513,220745  84% 30% 3% 3%
44Clojure #5 6.634.56562,080727  8% 54% 12% 74%
49Haskell GHC #2 3.152.85618,320919  77% 5% 27% 5%
55Erlang HiPE #4 45.0536.66689,3681167  77% 22% 9% 17%
60Erlang HiPE 21.6611.71762,6001302  80% 40% 26% 40%
62Python 3 #4 6.536.55781,144325  0% 1% 0% 100%
63Scala #7 5.463.11797,764949  46% 65% 38% 30%
73Python 3 #3 24.6224.65921,520295  0% 0% 1% 100%
81Erlang HiPE #3 61.0558.751,030,104624  4% 0% 1% 99%
89Dart #3 22.8022.611,122,456551  49% 5% 46% 2%
92Ruby JRuby #2 25.1019.651,166,576255  14% 12% 85% 18%
93Dart #2 34.3434.061,181,176555  47% 2% 30% 23%
Dart Failed443
Scala #6 Failed519
Scala #5 Failed329
"wrong" (different) algorithm / less comparable programs
37Python 3 #5 4.764.77471,320306
41Java  1.901.88512,576476
44Clojure #3 7.726.50555,744812
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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