Bioperl: article for Dr. Dobb's Journal

Lincoln Stein
Fri, 9 Oct 1998 15:56:19 -0400


Thanks for the pointer.  I'll use it in my discussions with the


Andrew Dalke writes:
 > Lincoln Stein <> said:
 > > Alternatively, I could focus on the alignment algorithm
 > > entirely, and this is what the editor has suggested.  I hate leaving
 > > out all the OO stuff, however.
 > I'm a bit surprised that they want to keep the alignment
 > algorithm.  I suppose I've been reading Dr. Dobb's too
 > long as I recall the April 1992 issue has a full article on
 > dynamic programming in the article "Finding String Distances"
 > (p56 if you still have it :)
 > It has a sub topic (two paragraphs) on "Comparing Genetic
 > Sequences", a description of how dynamic programming works,
 > a C implementation of the basic Levenshtein method, and
 > some discussion of speedups, including the statement "Molecular
 > biologists have taken these general-case algorithms and modified
 > them for specific circumstances, such as the FASTA family of
 > algorithms by Kipman and Pearson.  In these special cases,
 > complexity has been lowered to roughly O(m)."
 > For comparison, the source code is on-line at
 > 1992/1992.04/
 > which appears to be a somewhat different implementation than
 > yours.
 > Ewan Birney <> said
 > > To be honest I think the OOP stuff is more important than the
 > > algorithm and the fact that perl is the *ideal* language to glue
 > > and provide a development 'framework' is v. important.
 > *Ahem*.  You might want to stay away from religious issues like
 > that  :)  (I know, this is the bioperl list, but I'm here
 > because I want to keep up on computational chemistry and biology
 > development environments, even though I currently do most of my
 > programming in Python.)
 > > I'd go OOP-Perl to say that it is more than a web/systems
 > > glue language.
 >   But doesn't implementing alignment code in Perl shows that
 > just as well as showing it's use for OO development?  Still,
 > I would tend to agree that my interest is in how you set
 > up a large system using data encapsulation and all those other
 > CS buzzwords, which corresponds to the part:
 > > Programmers who prefer the object paradigm can use Perl to
 > > create object-oriented classes and methods.
 > Which to me is a more important thing than the details of an
 > standard algorithm which are found in an earlier DDJ and in
 > Knuth.
 > 						Andrew Dalke
Lincoln D. Stein                           Cold Spring Harbor Laboratory			                  Cold Spring Harbor, NY
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