[Bioperl-l] Bio::Graphics and primer3 pipeline

[Nathan Haigh]

Are these not parsed out of the primer3 output file at all, without the need
for actually calculating them? There seems to be quite a few useful
annotations that could be extracted from the output file.

Nath

-----Original Message-----
From: Rob Edwards [mailto:rob at salmonella.org] 
Sent: 16 July 2005 16:07
To: n.haigh at sheffield.ac.uk
Cc: 'Bioperl list'
Subject: Re: [Bioperl-l] Bio::Graphics and primer3 pipeline

You should be able to get the primers Tm from the  
Bio::SeqFeature::Primer objects - there are two different methods in  
there for calculating Tm's. The GC content is not a method at the  
moment, but could be added as one.

Rob


On Jul 15, 2005, at 5:43 AM, Nathan Haigh wrote:

> I'm creating a pipeline for passing around 200 sequences to primer3  
> in order
> to generate primers. I want to be able to use Bio::Graphics to  
> create a png
> file for each sequence with the position of the primers shown and  
> some of
> the details about each primer (e.g. Tm, %GC).
>
>
>
> Here's what I have so far in pseudocode:
>
>
>
> Foreach Bio::Seq object
>
>     Add position of introns as Bio::SeqFeature::Generic features
>
>     Run Primer3 with Bio::Seq object
>
>     Loop through primers, returning a Bio::Seq::PrimedSeq object
>
>         Add primer as features using: Bio::Seq
> object->add_SeqFeature(Bio::Seq::PrimedSeq);
>
>
>
> Now create png using Bio::Graphics
>
>
>
> This works ok, but I'm lost trying to get the Tm and GC content of the
> primers as returned by Primer3
>
>
>
> Does anyone have a script that can do something similar that I  
> might try to
> work out whats going on?
>
> Thanks
>
> Nathan
>
>
>
>
>
>
>
> ----------------------------------
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> Nathan Haigh
>
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>
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