[Biococoa-dev] Digest tool
Koen van der Drift
kvddrift at earthlink.net
Sat Feb 26 23:17:08 EST 2005
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:
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?
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