Random nucleotide string generator?

[Roger Hall]

All,
 
Is there a random generator for creating nucleotides (of length l with composition frequencies a, c, g, and t) in there somewhere?
 
I noticed a thread about it from 2000 and nothing since (searching for "random sequence").
 
If not - what should the namespace be for such a module should it be undone and desirable?
 
TIA!
 
Roger
 
 
 
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[Aidan Budd]

a non-bioperl option would be to use something external like seq-gen or
similar - tools designed for outputing "random" sequences simulated over a
tree - one could simply sample a single simulated sequence at random from
the output alignment

On Fri, 26 Jun 2009, Roger Hall wrote:

> All,
>  Is there a random generator for creating nucleotides (of length l with
> composition frequencies a, c, g, and t) in there somewhere?
>  
> I noticed a thread about it from 2000 and nothing since (searching for "random sequence").
>  
> If not - what should the namespace be for such a module should it be undone and desirable?
>  
> TIA!
>  
> Roger
>  
>  
>  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

--
----------------------------------------------------------------------
Aidan Budd                                    tel:[phone]
EMBL - European Molecular Biology Laboratory  fax:[phone]
Meyerhofstr. 1, 69117 Heidelberg, Germany

http://www.embl-heidelberg.de/~budd/
http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html

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[Luis Miguel Rodríguez]

Dear all, dear Roger,
I'm not sure if there is such generator (I think so).  Anyway, if you flag
it as "undone and desirable", please take into account the possibility of
extend the generator for dinucleotides, particularly useful when working
with secondary structure of RNA molecules,

Cheers,

On Fri, Jun 26, 2009 at 8:28 AM, Roger Hall <rahall2@...> wrote:

> All,
>
> Is there a random generator for creating nucleotides (of length l with
> composition frequencies a, c, g, and t) in there somewhere?
>
> I noticed a thread about it from 2000 and nothing since (searching for
> "random sequence").
>
> If not - what should the namespace be for such a module should it be undone
> and desirable?
>
> TIA!
>
> Roger
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

--
Luis M. Rodriguez-R
[http://bioinf.uniandes.edu.co/~miguel/]
---------------------------------
Unidad de Bioinformática del Laboratorio de Micología y Fitopatología
Universidad de Los Andes, Colombia
[http://bioinf.uniandes.edu.co]


+ 57 1 3394949 ext 2619
lmrodriguezr@...
me@...

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[Dave Messina-3]

The Bioperl solution piggybacks on EMBOSS. See Chris Fields' comment on this
post from Neil Saunders' blog:
http://nsaunders.wordpress.com/2007/07/25/howto-generate-random-sequences-using-emboss-and-perl/


You can also do this outside of BioPerl using shuffle from Sean Eddy's SQUID
package, available here:
[ SQUID ftp site ] <ftp://selab.janelia.org/pub/software/squid/>

<ftp://selab.janelia.org/pub/software/squid/>

If not - what should the namespace be for such a module should it be undone
> and desirable?


Perhaps add it to Bio::SeqUtils?


Dave
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[Dave Messina-3]

[Forwarding Bruno's reply.... -Dave]
---------- Forwarded message ----------
From: Bruno Vecchi <vecchi.b@...>
Date: Fri, Jun 26, 2009 at 14:44
Subject: Re: [Bioperl-l] Random nucleotide string generator?
To: Dave Messina <David.Messina@...>


Here's a little script that I used for a somewhat related task. It produces
a randomized version of an input sequence (thus keeping the original's
composition). Maybe you could adjust it to your needs; providing an input
sequence with the desired length and composition you should get what you
want.

#!perl
use List::Util qw(shuffle);
use Bio::SeqIO;

my ($seqfile, $number) = @ARGV;

my $in = Bio::SeqIO->new(-file => $seqfile);
my $fh = Bio::SeqIO->newFh(-format => 'fasta');

my $seq = $in->next_seq;
my @chars = split '', $seq->seq;

for my $i (1 .. $number) {
    @chars = shuffle @chars;
    my $new_seq = Bio::Seq->new(-id => $i, -seq => join '', @chars);
    print $fh $new_seq;
}

You can use it like this from the command line (assuming you want 20 output
sequences):

shuffle.pl input_sequence.fasta 20 > random_sequences.fasta

Bruno.

2009/6/26 Dave Messina <David.Messina@...>

> The Bioperl solution piggybacks on EMBOSS. See Chris Fields' comment on
> this
> post from Neil Saunders' blog:
>
> http://nsaunders.wordpress.com/2007/07/25/howto-generate-random-sequences-using-emboss-and-perl/
>
>
> You can also do this outside of BioPerl using shuffle from Sean Eddy's
> SQUID
> package, available here:
> [ SQUID ftp site ] <ftp://selab.janelia.org/pub/software/squid/>
>
> <ftp://selab.janelia.org/pub/software/squid/>
>
> If not - what should the namespace be for such a module should it be undone
> > and desirable?
>
>
> Perhaps add it to Bio::SeqUtils?
>
>
> Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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[Mark A. Jensen]

You guys earned your scrap:
http://www.bioperl.org/wiki/Random_sequence_generation

cheers and thanks! MAJ
----- Original Message -----
From: "Roger Hall" <rahall2@...>
To: <bioperl-l@...>
Sent: Friday, June 26, 2009 2:28 AM
Subject: [Bioperl-l] Random nucleotide string generator?

> All,
>
> Is there a random generator for creating nucleotides (of length l with
> composition frequencies a, c, g, and t) in there somewhere?
>
> I noticed a thread about it from 2000 and nothing since (searching for "random
> sequence").
>
> If not - what should the namespace be for such a module should it be undone
> and desirable?
>
> TIA!
>
> Roger
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>

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[Ocar Campos-2]

Thanks for the add to the wiki Mark.

Cheers.

O'car Campos C.
Bioinformatics Engineering Student.
University of Talca.


2009/7/1 Mark A. Jensen <maj@...>

> You guys earned your scrap:
> http://www.bioperl.org/wiki/Random_sequence_generation
>
> cheers and thanks! MAJ
> ----- Original Message ----- From: "Roger Hall" <rahall2@...>
> To: <bioperl-l@...>
> Sent: Friday, June 26, 2009 2:28 AM
> Subject: [Bioperl-l] Random nucleotide string generator?
>
>
>
>  All,
>>
>> Is there a random generator for creating nucleotides (of length l with
>> composition frequencies a, c, g, and t) in there somewhere?
>>
>> I noticed a thread about it from 2000 and nothing since (searching for
>> "random sequence").
>>
>> If not - what should the namespace be for such a module should it be
>> undone and desirable?
>>
>> TIA!
>>
>> Roger
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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