[Biococoa-dev] Digest tool

Alexander Griekspoor mek at mekentosj.com
Sun Feb 27 07:55:00 EST 2005

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: 
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).
- 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
- DNA can be circular, meaning that one has to account for potential 
cuts in the connecting segment if circularity is the case
- 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...

On 27-feb-05, at 5:17, Koen van der Drift wrote:

> Hi,
> I am going to work on the BCToolDigest class and need some feedback 
> from the DNA/RNA folks. I already have code to digest a protein, and 
> can add that without much problems. However, I would like to try to 
> make the class as universal as possible, so it should also work for 
> DNA and RNA. The code that I already have will digest a protein, based 
> on information of an enzyme that is stored in a plist file. An example 
> is:
> 	<key>Trypsin</key>
> 	<dict>
> 		<key>CleaveAt</key>
> 		<string>KR</string>
> 		<key>DontCleaveAdjacentTo</key>
> 		<string>P</string>
> 		<key>CleaveDirection</key>
> 		<string>C</string>
> 	</dict>
> So it defines the name of the enzyme in the key, and then identifies 
> where to cleave the protein, in this case at a lysine or arginine 
> residue. The string can contain more than one residues. It also adds 
> the possibility to define a residue that inhibits the cleavage if it 
> is adjacent to the given residue(s). Finally it defines on which side 
> of the residue to cleave.
> So my question is, when digesting an DNA/RNA, can I use a similar 
> approach? I have absolutely no clue about the digestion of DNA/RNA, so 
> the mechanism could well be completely different. In that case 
> additional class needs to be written, and maybe a super class to hold 
> code that is in common.
> The result of the code I already have is an array of subsequences. 
> Will the result of a DNA/RNA digest be similar?
> thanks,
> - Koen.
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                     ** Alexander Griekspoor **
              The Netherlands Cancer Institute
              Department of Tumorbiology (H4)
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                    Tel:  + 31 20 - 512 2023
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                   AIM: mekentosj at mac.com
                    E-mail: a.griekspoor at nki.nl
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