[Bioperl-l] K-mer generating script

[Brian Osborne]

Good idea.

I have a bunch of regular expressions for sequence searching, I think  
I'll put them into this Scrapbook category.

Brian O.


On Dec 20, 2008, at 1:34 AM, Mark A. Jensen wrote:

> Jason -
> Have a look at
> http://www.bioperl.org/wiki/Category:Scrapbook
> could be cool-
> MAJ
> ----- Original Message ----- From: "Jason Stajich" <jason at bioperl.org>
> To: "Mark A. Jensen" <maj at fortinbras.us>; "Blanchette, Marco" <MAB at stowers-institute.org 
> >
> Cc: "bioperl list" <bioperl-l at lists.open-bio.org>
> Sent: Saturday, December 20, 2008 12:02 AM
> Subject: Re: [Bioperl-l] K-mer generating script
>
>
>> Does someone want to put this on the wiki too?
>>
>> Maybe we could start a little bit of perl snippets for examples  
>> like  these.
>>
>> -j
>> On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote:
>>
>>> A little sloppy, but it recurses and is general---
>>>
>>> # ex...
>>> @combs = doit(3, [ qw( A T G C ) ]);
>>> 1;
>>> # code
>>>
>>> sub doit {
>>>  my ($n, $sym) = @_;
>>>  my $a = [];
>>>  doit_guts($n, $sym, $a, '');
>>>  return map {$_ || ()} @$a;
>>> }
>>>
>>> sub doit_guts {
>>> my ($n, $sym, $store, $str)  = @_;
>>> if (!$n) {
>>>  return $str;
>>> }
>>> else {
>>>  foreach my $s (@$sym) {
>>>    push @$store, doit_guts($n-1, $sym, $store, $str.$s);
>>>  }
>>> }
>>> }
>>>
>>>
>>> ----- Original Message ----- From: "Blanchette, Marco" <MAB at stowers-institute.org
>>> >
>>> To: <bioperl-l at lists.open-bio.org>
>>> Sent: Friday, December 19, 2008 6:25 PM
>>> Subject: [Bioperl-l] K-mer generating script
>>>
>>>
>>>> Dear all,
>>>>
>>>> Does anyone have a little function that I could use to generate  
>>>> all possible k-mer DNA sequences? For instance all possible 3-mer  
>>>> (AAA,  AAT, AAC, AAG, etc...). I need something that I could  
>>>> input the  value of k and get all possible sequences...
>>>>
>>>> I know that it's a problem that need to use recursive  
>>>> programming  but I can't get my brain around the problem.
>>>>
>>>> Many thanks
>>>>
>>>> Marco
>>>> --
>>>> Marco Blanchette, Ph.D.
>>>> Assistant Investigator
>>>> Stowers Institute for Medical Research
>>>> 1000 East 50th St.
>>>>
>>>> Kansas City, MO 64110
>>>>
>>>> Tel: 816-926-4071
>>>> Cell: 816-726-8419
>>>> Fax: 816-926-2018
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
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>>
>> Jason Stajich
>> jason at bioperl.org
>>
>>
>>
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>
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