[Biococoa-dev] Digest tool

[Koen van der Drift]

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: 
> http://www.mekentosj.com/enzymex/science.html

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 
those.


> - 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.


- Koen.