How can one randomize a DNA string without changing the composition?

supriyoch_2008 has asked for the wisdom of the Perl Monks concerning the following question:

Hi PerlMonks,

I am interested to randomize a DNA string in such a way that the number and the composition of elements in the DNA string remian the same but only the positions of elements are changed. For instance, I have a DNA string like "AATTGGCC" i.e. each base (A,T,G,C) has two copies. I want to get all possible combinations like ATATGGCC,AATGTGCC,ATATGCGC..etc. I am at a fix to find all the possible combinations from the string in perl. I looked for online resouces but I could not find the solution. I welcome suggestions from perlmonks. I have written a script which goes as follows. I have not written the code for combinations.

#!/usr/bin/perl
use warnings;

 my $dna="aattggcc"; 
 $dna=uc$dna; 
print "\n dna: $dna\n";

# code for all possible combinations ? 

exit;
[download]

Results should look like:

 All possible combinations are:
 ATATGGCC
 AATGTGCC
 ATATGCGC
 ........
[download]

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Re: How can one randomize a DNA string without changing the composition? by QM (Parson) on Jan 16, 2015 at 10:46 UTC
You might be interested in a small pure Perl solution, which I stole from a QOTW entry (which I can't locate). `# Find and return the $n'th permutation # of the remaining arguments in some canonical order # (modified from QOTW solution) sub permutation_n { my $n = shift; my $result = ''; while (@_) { ($n, my $r) = (int($n/@_), $n % @_); $result .= splice @_, $r, 1; } return $result; }` [download] -QM -- Quantum Mechanics: The dreams stuff is made of	[reply] [d/l]
Re^2: How can one randomize a DNA string without changing the composition? by Anonymous Monk on Jan 16, 2015 at 11:36 UTC
cough well thats certainly shorter than the solutions from 2012 How can one generate all possible combinations with reference to string positions?	[reply]
Re^3: How can one randomize a DNA string without changing the composition? by QM (Parson) on Jan 16, 2015 at 11:44 UTC
Thanks. There is a similar version, I recall, which just returns the next permutation, or can be turned into an iterator. For some reason I think I saw them on something MJD wrote, but it may originate from someone else through him. -QM -- Quantum Mechanics: The dreams stuff is made of	[reply]
Re: How can one randomize a DNA string without changing the composition? by Anonymous Monk on Jan 16, 2015 at 02:32 UTC
magic word you're looking for is "permutation", so permut, permut, permut	[reply]
Re^2: How can one randomize a DNA string without changing the composition? by Anonymous Monk on Jan 16, 2015 at 02:39 UTC
oh, its the question that never ends :) How can one get the correct results of all combinations with bigger input files? How to get non-redundant DNA sequences from a FASTA file? How can one find unique elements from arrays using a LOOP? How can one get all possible combinations of a string without changing positions & using window size?	[reply]
Re: How can one randomize a DNA string without changing the composition? by karlgoethebier (Abbot) on Jan 16, 2015 at 10:35 UTC
My first bioperl: `perl -MMath::Permute::List -e "permute {print qq(@_\n)} qw(A A T T G G C C);"` Best regards, Karl Update: I don't know if that is what you need because i'm no biologist :-( P.S.: Change ticks to ' if not on windoz. Update 2: Perhaps i missed something essential in your specs: "...the composition of elements in the DNA string remain the same" What does that mean? And the missing link: Math::Permute::List. ŤThe Crux of the Biscuit is the Apostropheť	[reply] [d/l]