Bioperl: article for Dr. Dobb's Journal
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 <email@example.com> 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
> which appears to be a somewhat different implementation than
> Ewan Birney <firstname.lastname@example.org> 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
> Andrew Dalke
Lincoln D. Stein Cold Spring Harbor Laboratory
email@example.com Cold Spring Harbor, NY
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