[Bioperl-l] modules for siRNA design

[Donald Jackson]

San and Heikki,

I've modified the SiRNA.pm module to fixed the bug per Heikki's suggestion.  I also added a sanity check in case the sequence is so short that the start_pad and end_pad values don't leave room for an oligo, and I added a feature to allow oligo design in the 3 prime UTR.  The mods just went into CVS as version 1.7

San - I strongly suggest that you give the module a longer target sequence if at all possible!

Don Jackson

----- Original Message -----
From: Heikki Lehvaslaiho <heikki at ebi.ac.uk>
Date: Monday, March 8, 2004 12:03 pm
Subject: Re: [Bioperl-l] modules for siRNA design

> San Wang,
> 
> The code in SiRNA.pm around line 263 looks like this:
> 
>    if ($cds) {
> 	$left = $cds->start + $self->end_pad;
> 	$right = $cds->end - $self->start_pad;	
>    }
>    else {
> 	$left = $target->start + $self->end_pad;    # line #263
> 	$right = $target->end - $self->start_pad;
>    }
> 
> Start and end calls are fine on a SeqFeature object like a CDS, but 
> are not 
> defined for a sequence. These lines  should be replaced by 
> something like the 
> following:
> 
> 	$left = 1 + $self->end_pad;
> 	$right = $target->length - $self->start_pad;
> 
> Your example sequence is not too realistic, so you'll get an other 
> error 
> caused by the shortness of the sequece. Call 
> 
> $sirna_designer->start_pad(0);
> $sirna_designer->end_pad(0);
> 
> before calling design().
> 
> Yours,	
>        	-Heikki
> 
> On Saturday 06 Mar 2004 19:08, ??, San Wang wrote:
> > Dear bioperl-l:
> >
> > 	I have report a bug for it.
> > "Can't locate object method "start" via package "Bio::Seq::RichSeq"
> > (perhaps you forgot to load "Bio::Seq::RichSeq"?) at
> > D:/Tools/perl/site/lib/Bio/Tools/SiRNA.pm line 263."
> >
> > 	Best Regards!
> >
> >                 	Yours sincerely
> > ??????????, San Wang
> > ????????bsman at tom.com
> > ??????????2004-03-07
> >  ,-,-.     ,-,-.     ,-,-.     ,-,-.     ,-
> > / / \ \   / / \ \   / / \ \   / / \ \   / /
> >      \ \ / /   \ \ / /   \ \ / /   \ \ / /
> >       `-'-'     `-'-'     `-'-'     `-'-'
> >
> >
> > San Wang
> > Dr. Student
> > Bioinformatics and Gene Network Research Group
> > Zhejiang University
> > P.R.China
> >
> > Address:
> > Room 415# ,Bio-technology Institute,
> > Zhejiang University,
> > Kaixuan Road 268#  Hangzhou
> > Zhejiang, P.R.China
> > 310027
> >
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> > Fax:
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> > Website:
> > http://www.estarray.org
> >
> > ??????????
> >   Innovation is everything. When you are on the forefront, you 
> can see what
> > the next innovation needs to be? --- from Robert Noyce, Founder 
> of Intel
> >   The more things change, the more they stay the same!
> >   The more things seem to be complicated ,the more they are 
> simple in fact!
> >
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> -- 
> ______ _/      _/_____________________________________________________
>      _/      _/                      http://www.ebi.ac.uk/mutations/
>     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
>    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
>