[Biopython] Adding a new restriction enzyme?

[Peter Cock]

On Thu Jul 31 05:40:52 UTC 2014, Mark Budde wrote:
>
> Hi,
> I would like to add the restriction enzyme I-SceI for use as a
> Bio.Restriction class. Would the best way to accomplish this be to import
> Bio.Restriction, then manually add I-SceI to
> Bio.Restriction.Restriction_Dictionary.rest_dict, using another enzyme as a
> template? Will that be sufficient?
> Thanks,
> Mark
>

Hi Mark,

The Bio.Restriction classes are auto-generated from REBASE,
http://rebase.neb.com/rebase/ - so first we would check if I-SceI
is defined there yet - and if so, update things.

This is done with Scripts/Restriction/rebase_update.py but
it can be a little fiddly if the new update includes evilly named
enzymes with minus signs or other funny characters.

However, I do not see I-Scel on their list:
http://rebase.neb.com/rebase/link_emboss_e
http://rebase.neb.com/rebase/link_emboss_s
http://rebase.neb.com/rebase/link_emboss_r

If this is a custom or in-house Enzyme, you can probably
just define it in your own Python script in a similar way...

See also this proposal to replace Bio.Restriction, comments
welcome: https://github.com/biopython/biopython/pull/268

Regards,

Peter