[Biococoa-dev] Digest tool
Koen van der Drift
kvddrift at earthlink.net
Sun Feb 27 08:29:42 EST 2005
On Feb 27, 2005, at 7:55 AM, Alexander Griekspoor wrote:
> Hmm, in principle there are many similarities so yes, we should try to
> make it work with DNA as well (don't know much about RNA cutting
> enzymes and their specificity...
> Don't want to sound to commercial (well, it's freeware anyway), but
> perhaps you can download our program EnzymeX
> (http://www.mekentosj.com/enzymex ) and play a bit with it. Also, Tom
> added in the help files quite some info on how these enzymes work.
> Finally, we have added a piece on our website about it:
Thank for the pointers - I'll check it out.
> Some potential pitfalls we have to foresee in the method:
> - DNA has two strands and enzymes can both generate blunt ends and
> overhangs (cut different position in the forward and reverse strand,
> see the picture of the enzyme sequence in enzymeX).
We should then first think about creating a double stranded BCSequence
object in BioCocoa. Once that is in place, we can think about digesting
> - Far more than is the case in peptide cleavage, ambiguity place a
> major role in DNA restriction enzymes: i.e. enzymes like EaeI that
> recognises: y^GGCCr
Right now I am using an NSScanner to identify the cleavage sites in a
sequence string. Then I use those sites to create subsequences. I
assume that NSScanner can be used for such ambiguous cases. What
approach are you guys using in EnzymeX to find the cleavage sites? BTW
is that supposed to be a regular expression?
> - DNA can be circular, meaning that one has to account for potential
> cuts in the connecting segment if circularity is the case
That's a tricky one, but as with the double stranded sequence, until we
have circular sequences in BioCocoa probably not so urgent.
> - Later on we can add the problem of methylation sensitivity, but
> that's way more advanced.
> I know John has created a DNA digestion plugin for 4Peaks, so he can
> tell you more probably. I'll send you the source off-list...
That would be great.
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