[Bioperl-l] Restriction Enzyme module?
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 v220.127.116.11,
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
University of Helsinki, | Mobile: 358-(0)50-336 8960
PL 56 | Home: 358-(0)9-728 7103
00014 Helsinki | email: Adrian.Goldman@Helsinki.fi
-- 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: email@example.com