[Bioperl-l] Restriction Enzyme cuts on Circular plasmids

[Jason Stajich]

On Wed, 29 Oct 2003, 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.
>
See http://doc.bioperl.org/bioperl-live for docs for code on the latest
CVS not the stable 1.2.x release series.

>
>
> 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/.
>

As Rob has said - it's new - not sure why the tutorial has been updated to
preceede the not-yet released code though.

>
>
> 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.
>

Bio::Seq is a Bio::PrimarySeq
http://doc.bioperl.org/releases/bioperl-1.2.3/Bio/PrimarySeqI.html#POD14

>
>
> 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?

http://search.open-bio.org/   ?  Seems to work just fine for me.  Putting
in 'Restriction' finds lots of hits and restricting that with 'Enzyme'
finds more hits too.

-jason
>
>
>
> -------------------------------------------------------------------------------------
> 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>
>
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu