[Bioperl-l] Bio::Restriction

Heikki Lehvaslaiho heikki at nildram.co.uk
Mon Dec 15 06:46:44 EST 2003


Great! Thanks, Rob and Peter!

	-Heikki

On Monday 15 Dec 2003 3:49 am, Rob Edwards wrote:
> I have just added the latest version of Bio::Restriction to cvs. The
> changes here are mainly to Restriction::Analysis, and should speed up
> looking at longer sequences, and adding functionality suggested by
> Peter.
>
> Restriction::Analysis should correctly handle the following:
>
> - overlapping sites
> - sites at or near the join points of circular sequences
> - non-palindromic restriction enzymes
> - enzymes that cut at more than one site
> - enzymes that cut more than once per site
>
> Restriction::Analysis should be more suitable for handling much larger
> sequences, using less memory and (hopefully) being faster than previous
> versions, especially for collections of non-ambiguous enzymes.
>
> The only thing that is stored for all enzymes are the cut positions
> (integers), and some statistics about how frequently each enzyme cuts
> and so forth. You can still get fragments and fragment maps out,
> they're just generated each time they are requested for each enzyme.
>
> The code should be cleaner and more readable too, now!
>
> I also fixed the tests that were failing with RestrictionIO.
>
> I removed the dependency on the caret (^) in the cut site, and now
> Analysis.pm just uses the values returned by cut and complementary_cut.
> Next on the list is to clean up Enzyme.pm and remove the caret unless
> it is essential.
>
> I also submitted the beginnings of a bairoch format rebase IO filter.
> This is barely limping in at the moment so use with caution, but this
> is the format that MacVector, VectorNTI, and PC/Gene support so I
> wanted to add this in.
>
> Rob
>
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     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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