[Bioperl-l] Restriction Enzyme cuts on Circular plasmids

[Rob Edwards]

The new Bio::Restriction modules should tell you the correct sizes of  
circular plasmids. This will do exactly what you want. The old  
Bio::Tools::RestrictionEnzyme does not have this ability, though you  
can just merge the first and last fragments of a sequence.

The newer Bio::Restriction are (I believe) only available in BioPerl  
1.3 and later. This is the upcoming release and the first RC seems  
quite stable.

You should probably tell someone about the searches not working, but I  
guess you just have :)

Rob



On Wednesday, October 29, 2003, at 10:39  AM, Gray, John wrote:

> I am trying to find documentation for the Bio::Restriction module, to  
> see if it can properly predict restriction fragment sizes for circular  
> plasmids.
>
>
>
> I'm sorry to have to ask.  The tutorial at  
> http://www.bioperl.org/Core/Latest/bptutorial.html says that  
> Bio::Restriction replaces the older Bio::RestrictionEnzyme, which I  
> have used.  I can't find any documentation for this method at  
> http://doc.bioperl.org/releases/bioperl-1.2.3/.
>
>
>
> The Seq documentation does not provide any description of the  
> 'is_circular' method, and I was hoping that I could set the Seq object  
> to be circular, and then just run something like  
> $enyme_object->cut_seq($seq_object) to get my list of strings  
> containing the resulting fragments.
>
>
>
> Thank you for your help.
>
>
>
> PS.  When I try and search the Bioperl-l archive, it doesn't return  
> any matches, even when I try to match the word 'bioperl'.  Should I  
> tell someone about this?
>
>
>
> ----------------------------------------------------------------------- 
> --------------
> John T. Gray, Ph.D.
> Director, Vector Development & Production
> Experimental Hematology Division
> Hematology-Oncology
> St. Jude Children's Research Hospital
> D2038A, Mail Stop 341
> 332 N. Lauderdale Street
> Memphis, TN 38105
>
> (901) 495-4729 phone
> (901) 495-2176 fax
>
> John.Gray at stjude.org <mailto:John.Gray at stjude.org>
>
>
>
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