[Bioperl-l] K-mer generating script

[Mark A. Jensen]

Prime mover was Jason- cheers all
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Blanchette, Marco" <MAB at stowers-institute.org>
Cc: "bioperl list" <bioperl-l at lists.open-bio.org>; "Mark A. Jensen" 
<maj at fortinbras.us>
Sent: Saturday, December 20, 2008 10:19 AM
Subject: Re: [Bioperl-l] K-mer generating script


> Added links to the main page and to the sidebar now.  Great idea Mark!
>
> chris
>
> On Dec 20, 2008, at 8:21 AM, Blanchette, Marco wrote:
>
>> This is a very good idea! I never realized this was on the BioPerl  website. 
>> Is there a clear link on the home page?
>>
>> Thanks to all, I have several very nice options.
>>
>> Cheers,
>>
>> Marco
>>
>>
>> On 12/20/08 12:34 AM, "Mark A. Jensen" <maj at fortinbras.us> 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
>>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Jason Stajich
>>> jason at bioperl.org
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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>>
>>
>> --
>> 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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