Bioperl: article for Dr. Dobb's Journal

Lincoln Stein
Mon, 12 Oct 1998 17:15:33 -0400

 > > Protein sequences use the letters
 > > A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,U,V,W, and Y. 
 > Remove U from this list. It represents selenocysteine which is not
 > part of the standard code. This would give you Gustavo's 20.

Ah ha!  I was wondering where my 21st amino acid came from.  So much
for copying codon tables out of other people's code.

 > > Sequence::Base
 > I would recommend changing this to Sequence::Generic since it is
 > possible to confuse this with a nucleotide base (AGCTU). You refer to
 > it later on as generic sequence class. (Incidentally, one may want a
 > class to represent a nucleotide base, especially when working
 > with structure.)

That's good.

 > > Unlike C++ or Java, Perl's object system allows for multiple
 > > inheritance, ...
 > C++ has multiple inheritence.

H'mmm.  Maybe I should say "usable" multiple inheritance?

Thanks for these and the other comments.


Lincoln D. Stein                           Cold Spring Harbor Laboratory			                  Cold Spring Harbor, NY
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