[Bioperl-l] Restriction Enzyme module?

Hilmar Lapp hlapp@gmx.net
Mon, 27 Nov 2000 23:38:07 -0800

> Subject: [Bioperl-l] Restriction Enzyme module?
> Date: Fri, 24 Nov 2000 10:50:42 -0500
> From: Adrian Goldman <agoldman@bnl.gov>
> To: bioperl-l@bioperl.org
> References: <200011241544.KAA19184@pw600a.bioperl.org>
> Hi,
>         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
> says.)
>         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?

SteveC is apparently unavailable. What I figured out is that you're
probably referring to the method cuts_seq_at(). I don't know any details
of the code, but you may be better off not using this method, as it has
been dropped in the main development trunk, for a reason I don't know
... Try cut_seq() instead, which seems to have survived unchanged (and
there's no beer bet warning).

Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757