# [BioRuby] help to understand the codes

chen li chen_li3 at yahoo.com
Thu Jun 18 15:42:03 UTC 2009

```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
>

```

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