[BioRuby] help to understand the codes
Tomoaki NISHIYAMA
tomoakin at kenroku.kanazawa-u.ac.jp
Wed Jun 17 23:55:12 UTC 2009
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}$/i =~ target #which rule is
> for this line
is for rule 1
--
Tomoaki NISHIYAMA
Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan
On 2009/06/17, at 23:32, chen li wrote:
>
> Hi all,
>
> I read source codes in sirna.rb in Bioruby. It implements the codes
> based on the following 4 rules( I copy the ruels from the paper):
> These rules indicate that siRNAs which
> simultaneously satisfy all four of the following
> sequence conditions are capable of inducing highly
> effective gene silencing in mammalian cells:
>
> (i) A/U at the 5' end of the antisense strand;
> (ii) G/C at the 5' end of the sense strand;
> (iii) at least five A/U residues in the 5' terminal one-third of
> the antisense
> strand;
> and (iv) the absence of any GC stretch of more than 9 nt in length.
>
>
> And here are the codes:
> In sirna.rb
> # Ui-Tei's rule.
> def uitei?(target)
> return false unless /^.{2}[GC]/i =~ target #which rule is
> for this line ?
> return false unless /[AU].{2}$/i =~ target #which rule is
> for this line
>
> return false if /[GC]{9}/i =~ target # rule 4
>
> #rule 3
> one_third = target.size * 1 / 3
> start_pos = @target_size - one_third - 1
> remain_seq = target.subseq(start_pos, @target_size - 2)
> au_number = remain_seq.scan(/[AU]/i).size
> return false if au_number < 5
>
> return true
> end
>
>
> from these codes I don't think I understand how rule 1 and rule 2
> are implemented. I wonder if someone can explain them a little more.
>
>
> Thanks,
>
> Li
>
>
>
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