[Bioperl-l] primer parameters using primer3

[Roy Chaudhuri]

Hi Li,

I think the syntax you need is:

$primer3->add_targets(PRIMER_PRODUCT_SIZE_RANGE=>'490-510');

I guess you may also need to change the parameter PRIMER_PRODUCT_OPT_SIZE.

Incidentally, such a restricted product size range may mean that Primer3 
is unable to design any suitable primers. If I recall correctly, this 
doesn't cause an error, you just get a Bio::Tools::Primer3 object with 
no primers in it. I have had some success with testing for this, and if 
necessary relaxing some constraints on primer design and re-running 
Primer3.

Hope this helps.
Roy.

--
Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, U.K.

http://xbase.bham.ac.uk

> Hi Jason,
> 
> I add the line code   
> $primer3->primer_product_size_range("490-510");
>  to my script. But it doesn't work nor primer3
> complains it.
> 
> Li
> 
> --- Jason Stajich <jason.stajich at duke.edu> wrote:
> 
>> > I put up some info on the wiki (and I encourage
>> > other people to do  
>> > the same!)
>> >
> http://bioperl.org/wiki/Module:Bio::Tools::Run::Primer3
>> > 
>> > Set the command line parameters by just calling a
>> > function of the  
>> > name of the parameter.  To get a list of the
>> > available options, this  
>> > perl code will report it to you:
>> > 
>> > # what are the arguments, and what do they mean?
>> >    my $args = $primer3->arguments;
>> > 
>> >    print "ARGUMENT\tMEANING\n";
>> >    foreach my $key (keys %{$args}) {print "$key\t",
>> > $$args{$key}, "\n"}
>> > 
>> > The info for PRODUCT_SIZE_RANGE is:
>> >    (size range list, default 100-300) space
>> > separated list of product  
>> > sizes eg <a>-<b> <x>-<y>
>> > 
>> > I believe you can set the PCR product size with
>> >    $primer3->primer_product_size_range("490-510");
>> > 
>> > -jason
>> > On May 7, 2006, at 3:34 AM, chen li wrote:
>> > 
>>> > > Hi all,
>>> > >
>>> > > I use Bio::Tools::Run::Primer3 to design PCR
>> > primers.
>>> > > I want to change some default values, for example,
>> > to
>>> > > increase the PCR product size to 490-510 bp
>> > instead of
>>> > > using the default value of 100-300 bp. What should
>> > I
>>> > > do ?
>>> > >
>>> > >
>>> > > Thanks,
>>> > >
>>> > > Li
>>> > >
>>> > > __________________________________________________
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>> > 
>> > --
>> > Jason Stajich
>> > Duke University
>> > http://www.duke.edu/~jes12
>> > 
>> > 
>> > 
> 
> 
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