Bioperl: article for Dr. Dobb's Journal

Lincoln Stein
Sun, 11 Oct 1998 14:26:22 -0400

Gustavo Glusman writes:
 > >I'm writing an article for Dr. Dobb's Journal on Perl and Molecular
 > >Biology.
 > Reading it, a few comments -
 > * Why talk about 21 amino acids, when there are 20? I can understand the
 > expression 'the 21 letter alphabet', but a phrase like "The other thing to
 > notice is that certain codons (three in all) don't encode any amino acids."
 > certainly clashes with "the 21 amino acids"... Why not just talk about 20
 > amino acids and 3 termination codes?


 > * "For historical reasons, DNA subsequences use 1-based indexing,..."
 > -> For *historical* reasons??

Because people have always done it that way, even though it conflicts
with the more natural (to programmers) way of 0-based indexing.

 > * "there may be small differences between the two sequences, either
 > because of errors during the sequence determination or because they
 > are from different but related organisms"
 > -> Or because they're paralogues, or alleles. (I just suggest relaxing the
 > 'either...or' so it doesn't imply these are the two only reasons.)


 > * As for the length of the article, I agree that the dp section can go;
 > maybe just modify slightly the section on align() from "we'll look at this
 > utility class later" into something like "which is also implemented in
 > Perl". Conceivably even the section on subseqs could go, but IMHO it would
 > be more rewarding to trim on the side of what points the article conveys.
 > I'm just thinking about how many readers will react along the lines of "I
 > know Perl is good at doing such projects, and the bio stuff confuses me.
 > Other than claim that large projects can be done using such base classes,
 > have you really found out that it works well and it doesn't get too
 > sluggish as the project grows?"

Thanks for the helpful comments.


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