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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 2.0625,4481064  6% 26% 66% 61%
 OCaml #3 0.8912,6441314  52% 57% 83% 67%
 C gcc #2 0.920.67248,640741  15% 11% 79% 36%
 Fortran Intel 1.021.04246,4601013  1% 0% 1% 100%
 C gcc 1.160.85496,9401867  26% 0% 88% 27%
 C++ g++ #4 1.220.84245,4562275  29% 33% 49% 35%
 C++ g++ #2 1.291.02245,1281082  10% 9% 99% 12%
 Rust 1.331.33248,880804  0% 0% 100% 0%
 C gcc #4 1.341.34125,100704  0% 1% 1% 100%
 C++ g++ #3 1.341.34124,968810  1% 1% 0% 100%
 Haskell GHC #3 1.541.45125,956999  3% 6% 4% 100%
 Ada 2005 GNAT #2 1.641.24197,1243220  42% 1% 26% 64%
 OCaml #4 1.661.67127,5802064  0% 1% 1% 100%
 Go #3 1.821.82159,880543  2% 0% 0% 100%
 Java  #6 2.011.74513,220745  84% 30% 3% 3%
 Pascal Free Pascal #2 2.172.17122,544751  0% 0% 0% 100%
 Scala #8 2.201.69512,996761  92% 6% 33% 2%
 Go 2.281.93249,1641243  3% 16% 6% 98%
 Scala #4 2.482.41406,492501  2% 2% 98% 5%
 Go #2 2.522.52160,120546  0% 100% 0% 0%
 Java  #7 2.707.31264,9121640  28% 28% 18% 45%
 C# Mono 2.822.82171,2721099  1% 74% 2% 26%
 Perl #3 3.043.05374,472284  0% 1% 1% 100%
 Java  #4 3.143.04478,080592  3% 98% 2% 3%
 Haskell GHC #2 3.152.85618,320919  77% 5% 27% 5%
 Java  #3 3.161.63296,1361661  77% 24% 39% 58%
 C++ g++ 3.903.90245,220571  1% 1% 100% 0%
 Ada 2005 GNAT 4.144.15130,092885  0% 1% 100% 1%
 Lisp SBCL 4.304.31219,636896  0% 0% 0% 100%
 Racket #2 4.484.48172,5481026  1% 1% 100% 1%
 OCaml #2 4.494.50171,972394  0% 16% 84% 0%
 Scala #7 5.463.11797,764949  46% 65% 38% 30%
 Clojure 6.435.09405,1641044  11% 6% 98% 12%
 Python 3 #4 6.536.55781,144325  0% 1% 0% 100%
 Clojure #5 6.634.56562,080727  8% 54% 12% 74%
 PHP #2 7.837.85443,496262  0% 100% 0% 0%
 PHP 7.927.95370,544297  0% 13% 88% 0%
 Clojure #4 8.026.50446,884997  49% 8% 11% 58%
 Fortran Intel #2 8.288.30167,656772  0% 0% 0% 100%
 C# Mono #3 9.209.21255,164863  0% 100% 0% 0%
 Ruby #2 10.6110.62127,848255  0% 0% 100% 1%
 Racket 13.5813.59506,864547  0% 1% 100% 0%
 Erlang HiPE 21.6611.71762,6001302  80% 40% 26% 40%
 Dart #3 22.8022.611,122,456551  49% 5% 46% 2%
 Python 3 #3 24.6224.65921,520295  0% 0% 1% 100%
 Ruby JRuby #2 25.1019.651,166,576255  14% 12% 85% 18%
 C++ g++ #5 25.1825.19170,168646  1% 1% 100% 0%
 Dart #2 34.3434.061,181,176555  47% 2% 30% 23%
 Erlang HiPE #4 45.0536.66689,3681167  77% 22% 9% 17%
 Erlang HiPE #3 61.0558.751,030,104624  4% 0% 1% 99%
Dart Failed443
Scala #6 Failed519
Scala #5 Failed329
"wrong" (different) algorithm / less comparable programs
 Java  1.901.88512,576476
 Python 3 #5 4.764.77471,320306
 Clojure #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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