[Bioperl-l] primer parameters using primer3

[Brian Osborne]

Li,

Read the documentation, Bio::Tools::Run::Primer3. It shows examples of the
correct syntax. Also look at bioperl-run/t/Primer3.t.

Brian O.


On 5/7/06 9:18 PM, "chen li" <chen_li3 at yahoo.com> wrote:

> 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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