[Biococoa-dev] Digest tool

[Koen van der Drift]

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.