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

[Steve Chervitz]

RestrictionEnzyme doesn't support this behavior at present. In fact, it 
doesn't fully support restriction sites containing any ambiguity 
characters because it inserts ambiguity characters in place of the 
actual sequence at the ends of the fragments. If you're just interested 
in the sizes of the fragments, it should be fine, but if you want the 
actual sequence data in the fragments, you'll have to extract it from 
the original sequence yourself. See comments in 
RestrictionEnzyme::cut_seq() for more info as to why this is the case.

If you'd like to see better support for this, consider filing a bug 
report at bugzilla.bioperl.org, which can be used for feature requests, 
too.

Steve


On Thursday, Dec 26, 2002, at 21:28 US/Pacific, Alexander Gimelbrant 
wrote:

> 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?
>
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