[Bioperl-l] Specifying restriction enzyme with cut site outside recognition sequence

[Alexander Gimelbrant]

How does one specify an enzyme that cuts outside the recognition sequence?
e.g., AlwI:
Recognition Sequence: GGATC (4/5)
5' ..GGATCnnnn^nn..3'
3' ..CCTAGnnnnn^n..5'

An extremely naive attempt:
$re = new Bio::Tools::RestrictionEnzyme('-NAME' =>'Nnn--GGATCNNNN^N',
                                           '-MAKE' =>'custom');
Leads (rather unreasonably) to insertion of N's into the digested sequence
at cut sites.

An attempt to specify
$num = $re->cuts_after(9);
throws an exception, since you cannot set cut_after larger than length of
recognition sequence.

Any way around that?