[BioRuby] help to understand the codes

[Tomoaki NISHIYAMA]

Hi,

> but will not match the following nts:
> N---NA/UAT
> N---NA/UTA
>
> which mean the last two nts are identical, is that right?

.{2} is equivalent to ..
and should match any two characters, identical or different.

--  
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan


On 2009/06/19, at 0:42, chen li wrote:

>
> Hi Tomoaki,
>
> Thank you for the explanation.
>
> For rule 1: /[AU].{2}$/i =~ target
> Based on my understanding of regular expression, it will match the  
> following nts:
> N---NA/UAA
> N---NA/UTT
> N---NA/UGG
> N---NA/UCC
> but will not match the following nts:
> N---NA/UAT
> N---NA/UTA
>
> which mean the last two nts are identical, is that right?
> The similar situation applies to rule 2: /^.{2}[GC]/i =~ target
>   starting with two identical nts followed by G/C at the third  
> position.
>
> If this is the case I wonder where the paper mentions that the last  
> two nts are the same and the first two nts are identical. Do I miss  
> something when I read the paper?
>
>
>
> Thanks,
>
> Li
>
>
>
>
>
>
>
>
> --- On Wed, 6/17/09, Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa- 
> u.ac.jp> wrote:
>
>> From: Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp>
>> Subject: Re: [BioRuby] help to understand the codes
>> To: "chen li" <chen_li3 at yahoo.com>
>> Cc: "Tomoaki NISHIYAMA" <tomoakin at kenroku.kanazawa-u.ac.jp>,  
>> bioruby at lists.open-bio.org
>> Date: Wednesday, June 17, 2009, 7:55 PM
>> Hi,
>>
>> Perhaps, an implicit assumption is used that the siRNA
>> duplex
>> has 2 nt overhang at the 3' ends and the "target" is
>> written for one strand containing both:
>> So, the sequence should be
>> from the rule 1 and 2:
>>   SNNN...NNNNNNNNNNN
>> NNNNNN...NNNNNNNNW
>>
>> (W: A or U, S: G or C)
>>
>> from the compliment rule
>> this will be
>>   SNNN...NNNNNNNNWNN
>> NNSNNN...NNNNNNNNW
>>
>> and if you write only the top strand (or the original mRNA
>> sequence)
>> NNSNNN...NNNNNNNNWNN
>>
>> thus
>>>        return false unless
>> /^.{2}[GC]/i =~ target  #which rule is for this line ?
>> is for rule 2
>> and
>>>        return false unless
>> /[AU].{2}$/i =~ target   #which rule is for
>> this line
>> is for rule 1
>> --Tomoaki NISHIYAMA
>>
>> Advanced Science Research Center,
>> Kanazawa University,
>> 13-1 Takara-machi,
>> Kanazawa, 920-0934, Japan
>>
>
>
>
>