[Bioperl-l] Restriction Enzyme cuts on Circular plasmids

[Gray, John]

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>