[Bioperl-l] cut_seq in Bio::Tools::RestrictionEnzyme

Chris Fields cjfields at uiuc.edu
Thu Apr 6 12:48:56 EDT 2006


I believe Bio::Tools::RestrictionEnzyme is no longer maintained
(deprecated).  Use Bio::Restriction instead.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Staffa, Nick (NIH/NIEHS) [C]
> Sent: Thursday, April 06, 2006 9:25 AM
> To: bioperl-l
> Subject: [Bioperl-l] cut_seq in Bio::Tools::RestrictionEnzyme
> 
> Please help me to understand the working of
> cut_seq in
> http://doc.bioperl.org/bioperl-live/Bio/Tools/RestrictionEnzyme.html#POD7
> explicitly to extract the information contained in the return variable ---
> some sort of reference to something.
> Documentation says
> Title     : cut_seq
>  Usage     : $re->cut_seq(<sequence object>);
>  Purpose   : Conceptually cut or "digest" a DNA sequence with the given
> enzyme.
>  Example   : $string = $re->cut_seq(<sequence object>);
>  Returns   : List of strings containing the resulting fragments.
>  Argument  : Reference to a Bio::PrimarySeq.pm-derived object.
> 
> Eventually I want the length of the fragments.
> 
> 
> Thank you.
> 
> 
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
> 
> 
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