[Bioperl-l] Restriction Enzyme module?

Adrian Goldman agoldman@bnl.gov
Fri, 24 Nov 2000 10:50:42 -0500


	I am trying to write a program that "cuts" DNA using RE.pm -- 
and it works fine, but I have a few questions.  (I am using v1.4.2.1, 
at least that is what the header in BIO::Tools::RestrictionEnzyme.pm 

	First, the documentation has this disturbing comment "I 
*think* that this is right for non-palindromic enzymes like TspRI, 
but i wouldn't bet  a lot of beer on it."  Is it OK now?  Or do I 
need to check?

	Second, what about "offset cutters" like BseRI, where the cut 
site can not be described as a single integer in relationship to the 
sequence, as it cuts 10 bp to the 5' side of the forwad strand 
recognition site and 8 bp to the 3' site of the reverse strand 
recognition site?  Is this coded internally at all?  If so, how would 
I feed it in using the standard methods (-NAME=>... 

	Any help would be MUCH appreciated....

Professor Adrian Goldman,            | Phone:     358-(0)9-191 58923
Structural Biology Group,            | FAX:       358-(0)9-191 58952
Institute of Biotechnology           | Sec:	  358-(0)9-191 58921
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-- on sabbatical at Brookhaven National labs, June 2000-June 2001
Adrian Goldman, Biology Department, Building 463 50 Bell Ave., 
Brookhaven National Lab., Upton NY 11973.  Phone: 631-344-2671 (off) 
631-344-3417 (lab), 631-344-3407 (FAX).  email: agoldman@bnl.gov